Category Archives: Genome

A UB team has developed a new model of how information in the genome is organized, called the novel genome archipelago model (GAM). The model provides new insights into how a multitude of interactions among genes may affect normal development, as well as mutations that lead to cancer and other diseases.

GAM offers a physical basis for the idea of systems genomics, which has begun to emerge in recent years, in which individual genome elements are integrated into an organism-like entity, says Michal K. Stachowiak, professor in the Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences at UB.

Stachowiak is senior author on thepaper that describes the GAM, which was published in a special edition of the International Journal of Molecular Sciences entitled Molecular Mechanisms of Neural Stem Cells Systems Approach.

The study advances the idea that the GAM is created through the interactions of distant chromosome regions and even different chromosomes.

Stachowiak says the study shows that tens of thousands of genes may engage in hundreds of millions of interactions, and that through these associations, genomic function is executed.

This vast interactome, as we call it, truly constitutes a new code for the information that is stored and executed by the genome, he says.

The interactions were mapped by first author Brandon Decker when he was working in Stachowiaks laboratory as a graduate student in UBs Genetics, Genomics and Bioinformatics program. Decker is now a postdoctoral associate at the National Institute on Aging, part of the National Institutes of Health.

Stachowiak explains that the GAM is based on the idea that the genome is an archipelago of constantly changing islands, and that when the islands form, they provide a blueprint for specific parts of the body and specific functions.

A single small mutation may have broad impact on genomic function by disrupting multi-genome interactions or their control mechanism, he says. It is the understanding of these interactions that may bring our therapeutic efforts to new, unprecedented levels.

Stachowiak says they assign the central role in organizing the GAM to a nuclear form of the protein FGFR1, which, through its Integrative Nuclear FGFR1 Signaling (INFS) mechanism, discovered in his lab, offers a new paradigm for genomic regulation of an organisms development. He notes that recent studies by teams at other institutions have shown that INFS plays an important role in cancers, including breast cancer.

This is an example of how an advanced basic science becomes translated into clinical medicine andmay offer new strategies for cancer treatments, he says.

Stachowiak named his model to reflect his lifelong inspiration by the travels of Charles Darwin, who developed his theory of evolution after happening upon the islands of Galapagos. We refer to different islands that form in the cell nucleus and, as we propose, orchestrate ontogenesis, Stachowiak says.

In addition to Decker and Stachowiak, other UB authors are Yongho Bae and Ewa Stachowiak, both of the Department of Pathology and Anatomical Sciences; Josep M. Jornet, associate professor of electrical engineering at Northeastern University; and Donald Yergeau, associate director of genomic technologies in UBs New York State Center of Excellence in Bioinformatics and Life Sciences.

Co-authors are Hussam Abdellatif, a doctoral student at the Institute for the Wireless Internet of Things at Northeastern University, who trained with Jornet, and Michal Liput, a doctoral student at the Mossakowski Medical Research Center, Polish Academy of Sciences, who trained with Stachowiak at UB.

This research was funded by three consecutive grants from the National Science Foundation, with additional support from New York State Department of Health and the Patrick P. Lee Foundation.

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UB team proposes genome 'archipelago' as new model of how genomic information influences development, disease - UB Now: News and views for UB faculty...

Genetic "dark matter" may drive the emergence of new species, new research finds.

These long, repeating stretches of the genome, called satellite DNA, may ultimately prevent incompatible animals from mating by scrambling the chromosomes in their hybrid babies, according to the study. And if animals from different populations can't mate, they will diverge over time, leading to speciation.

Just 1% of the 3 billion letters, or nucleotides, in the human genome make the proteins that determine traits such as eye color and height. Other stretches of DNA may tell the body how many copies of a protein to make, or turn genes on or off in different tissues, among other functions. Yet nearly 10% of the human genome is composed of long, repeating stretches of satellite DNA that, for many years, scientists didn't think did much of anything, said study co-author Madhav Jagannathan, currently an assistant professor at the ETH Zurich Institute of Biochemistry in Switzerland.

Related: Genes of 500-million-year-old sea monsters live inside us

"Satellite DNA repeats were very abundant in species and widely observed in eukaryotes," or life-forms with cell nuclei, Jagannathan told Live Science in an email. "Despite this, they were largely dismissed as junk DNA."

However, in a 2018 study, Jagannathan, who was then at the Massachusetts Institute of Technology (MIT), and his former postdoctoral adviser, biologist Yukiko Yamashita, also at MIT, discovered that some of this DNA served a critical purpose: It organizes DNA within a cell's nucleus. That study found that certain proteins grab DNA molecules and arrange them in densely packed bundles of chromosomes called chromocenters. Satellite DNA, they found, tells these grabby proteins how to bundle and organize chromosomes.

In the newest study, published July 24 in the journal Molecular Biology and Evolution, Jagannathan and Yamashita found another role for satellite DNA: driving speciation. The team was investigating fertility in the fruit-fly species Drosophila melanogaster. When the researchers deleted a gene that codes for a protein called prod, which binds to satellite DNA to form chromocenters, the flies' chromosomes scattered outside the nucleus. Without the ability to correctly organize chromosomes, the flies died.

This was fascinating, Jagannathan said, because the deleted protein is unique to D. melanogaster. That meant that these rapidly evolving satellite DNA sequences must also have rapidly evolving proteins that bind to them.

To test this idea, Jagannathan bred D. melanogaster females with males of a different species, Drosophila simulans. As expected, the hybrids did not live long. When the researchers looked into the flies' cells, they saw misshapen nuclei with DNA scattered throughout the cells, just as they had when they deleted the prod protein in previous experiments.

So why does that mean satellite DNA could drive speciation? The team suspects that, if satellite DNA evolves quickly and two creatures make different satellite-DNA-binding proteins, they won't produce healthy offspring. As chromocenter binding proteins and satellite DNA segments evolve differently in separate populations or species, this incompatibility could arise rather quickly.

To test this hypothesis, they mutated satellite DNA-binding genes that led to the incompatibility in both parents. When they rewrote the flies' genomes to be compatible, they produced healthy hybrids.

Such satellite DNA disagreements could be a big factor in the evolution of new species, Jagannathan suspects. He hopes further research can test their model of hybrid incompatibility with other species. Ultimately, this research could lead to a way for scientists to rescue "doomed" hybrids, or hybrids that don't survive long after birth. This could pave the way for using hybridization as a method for rescuing critically endangered species, such as the Northern White Rhino, of which only two females survive.

Ultimately, the new research confirmed Jagannathan's hunch that satellite DNA served a purpose.

"I thought that there was no way evolution could be so wasteful," Jagannathan said.

Originally published on Live Science.

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Dark regions of the genome may drive the evolution of new species - Livescience.com

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A genomic sequencing report submitted to the Karnataka government has suggested that the SARS-CoV-2 virus is changing. Currently, the Delta and sub-lineages of Delta are spreading across Bengaluru Urban and picking up new mutations.

The report said that of these mutations, the N439 mutant has already exhibited the potential to increase the fitness of the virus.

The report cautioned: "We need to monitor any increase in the frequency of these mutations. As that might be a signal for a new variant, which may not be covered by the protection from vaccines," the report quoted in bold letters.

This report comes ahead of a similar account of results of 300 samples sent for genomic sequencing that is expected to be released soon. The results will be discussed by the Committee for COVID-19 Whole Genome Sequencing (WGS), which is to meet on Thursday for discussing the findings.

Strand Precision Medicine Sciences, a genomics-based research and diagnostics company mandated to conduct genomic sequencing by the Karnataka government to help detect trends in mutations, has submitted its report to the health ministry on September 1.

The report has also been sent to the Karnataka Covid Task Force, Chairman of Genomic Surveillance Committee, Karnataka; Bruhat Bengaluru Mahanagara Palike (BBMP) Commissioner and health commissioner BBMP.

Samples processed include 34 sequences from children, 28 sequences from partially and fully vaccinated individuals, and 6 from fully vaccinated individuals. The investigations were conducted on 298 complete sequences.

The outputs suggested the identification of four lineages, and all were Delta or sub-lineages of Delta. The report also said three lineages of Delta and two sub-lineages of Delta AY.4 and AY.12 were found across all groups of Bengaluru Urban.

The report also spoke about new mutations. "This sequencing showed 133 mutations in spike protein alone. Many of these are known mutations," the report said.

"We found several new mutations at low frequency (0.3%

N439K mutant found in 7 sequences, N440Y/T/F mutant in 8 sequences, L441Y/S/G/A/C/D/V found in 7 sequences, D4421/V/Y/F in 9 sequences, S443E/V/Y/W/F in 7 sequences, K444F/N/V/T/S/V mutants found in 7 sequences.

However, experts opine that genomic sequencing results are not a cause for worry as most samples are collected from persons treated at home.

Strand Precision Medicine Solutions was tasked with studying mutations through genome sequencing by the Covid Task Force in Karnataka. The sequencing indicated 30% mutation in the Delta AY.4 variant and 3% in AY.12 mutant.

Total 298 swabs were collected from COVID-19 patients in Bengaluru for genomic sequencing. It also showed that Delta and its sub-lineages AY4 & A12 were dominant across different age groups in Bengaluru.

The test also showed that the COVID-19 virus was changing and Delta's sub-lineages are spreading across Bengaluru urban areas with new mutations being reported.

**

The above article has been published from a wire agency with minimal modifications to the headline and text.

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Genome Sequencing Results Show that SARS-CoV2 is Picking Up New Mutations in Karnataka | The Weather Channel - Articles from The Weather Channel |...

By analysing genomic data from more than 30,000 people, an international research team has revealed thousands of new regulatory regions that control disease-linked genes. Their findings, published in the journal Nature Genetics, have been described as a significant step forward for genomics-driven precision medicine and could help identify markers that reveal which patients will benefit most from which treatment.

In this study we have provided an entirely new view of genetic regulation by uncovering an in-depth picture of how genes and disease are linked, said co-senior author Associate Professor Joseph Powell, Director of the Garvan-Weizmann Centre for Cellular Genomics and Deputy Director of the UNSW Cellular Genomics Futures Institute. It is the most comprehensive analysis of how human genetic variation affects gene expression to date.

To study how human genetic variation affects our risk of disease, researchers often carry out genome-wide association studies, which scan the genomes of patients and look for genetic variants more commonly associated with a specific condition. But interpreting these results is not straightforward instead of directly driving disease, many genetic variants instead regulate the activity of genes, influencing how much of a protein is produced.

By pinpointing these regulatory regions, known as expression quantitative trait loci (eQTLs), researchers are able to better understand which genes directly contribute to disease risk and which could be targeted with precision treatments. In this study, the team used specialised machine learning algorithms to analyse genomic data from the blood samples of 31,684 individuals.

Thanks to the statistical power of this large dataset, we were able to uncover new regulatory regions on the human genome, Assoc Prof Powell said. Instead of just cataloguing the regulatory gene locations that were adjacent (known as cis-eQTLs), we were able to reveal genes that modulated the activity of more distant genes (known as trans-eQTLs).

Out of the millions of genes they investigated, the researchers found not only that 88% had a cis-eQTL effect, but that 32% of genes also had a trans-eQTL effect further away in the genome, more than half of which they could assign to a biological impact, such as cardiovascular and immune diseases.

While its clear that genetic variants are almost always a root cause of disease, the mechanism by which they influence disease is far less clear, Assoc Prof Powell said. For instance, while a specific condition may be linked to hundreds of genetic variants, the vast majority contribute to disease by regulating gene activity.

Understanding which genes this regulation converges on will be invaluable to identify targets for new potential medicines. If a pharmaceutical company develops a therapy that targets a certain molecule, our resource can help identify how its expression is regulated and if the genetic background of different patients is likely to impact its efficacy.

What weve discovered is an entirely new level of genomic information, providing a deeper understanding of biology and disease.

The teams resource is now available to researchers worldwide via http://www.eqtlgen.org.

Image credit: stock.adobe.com/au/Tartila

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New regulatory regions uncovered on the human genome - Lab + Life Scientist

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (375 Mya) or the evolution of arboreal vertebrate species (160 Mya). When divergent lineages transition to the same novel habitat, it provides an opportunity to investigate the mechanisms that permit these adaptations and the relationship between similar phenotypes among lineages and the underlying genetic basis. Convergent processes may utilize homologous genomic regions in different lineages to achieve similar phenotypes (1). Alternatively, distinct, genomic processes may be possible (2), or genetic drift may lead to different options for divergent lineages. Relatively recent transitions may be the most informative, on the assumption that extended periods of evolution may obscure the relationship between genomic differences and the original adaptations. A system well suited to this investigation is the adaptation of divergent, terrestrial mammalian lineages to life in aquatic environments.

Marine mammals, broadly defined as mammals whose terrestrial predecessors entered the sea and who obtain all or most of their food from a marine environment, comprise at least 129 extant species divided into three orders (3). Cetartiodactyla includes cetaceans (whales, dolphins, and porpoises); Carnivora includes pinnipeds (walruses, sea lions, and seals), sea otters, and polar bears; and Sirenia includes sea cows (now extinct), manatees, and dugongs (3). Of these, cetaceans, pinnipeds, and sirenians are considered the oldest groups of marine mammals (3). In contrast, sea otters and the polar bear emerged relatively recently so much so that the polar bear can still hybridize with terrestrial sister taxa (35). The most species-rich group of marine mammals is Cetacea, which comprises 90 species (3). Cetaceans, pinnipeds, and sirenians represent an exceptional case of convergent evolutionthe emergence of similar phenotypic traits in species separated by millions of years of evolution (6). In these separate lineages of marine mammals, phenotypic convergence is observed in all major physiological systems (7, 8). The degree to which convergence is reflected at the molecular level can now be partially answered using genomics. However, the interpretation of such results has hitherto been restricted by the limited number of high-quality genomes from marine mammals (6, 9). Remaining uncertainties include the phylogenetic relationships between and within marine mammal groups and their demographic history. To address these questions, we assembled and annotated 17 marine mammal genomes (11 cetaceans and six pinnipeds). Based on more comprehensive genomic data, we identified many putative genetic innovations for the aquatic adaptation of mammals, including those associated with thermoregulation and skeletal systems.

We performed the sequencing and de novo assembly of 17 marine mammal genomes (11 cetaceans and six pinnipeds) (SI Appendix, Table S1). Among these, 14 were assembled by Supernova (10) with 10 Genomics data (average scaffold N50 = 28.66 Mb and contig N50 = 142.33 kb) (Table 1 and SI Appendix, Tables S1S3). The remaining three genomes were assembled using Illumina paired-end reads (SI Appendix, Tables S1S3). Eight of the assemblies were further improved by Hi-C chromosome anchoring (SI Appendix, Fig. S1). The assembled genomes of the 17 marine mammal species range in size from 2.37 to 2.62 Gb, which is similar to k-merbased estimations using GCE (11) (SI Appendix, Table S4) and those of published marine mammal genomes (SI Appendix, Table S5). More than 95% of each species short reads could be mapped to their respective assembly (SI Appendix, Fig. S2). BUSCO (Benchmarking Universal Single-Copy Orthologs) (version 3.0.2) (12) was used to assess the quality of the assemblies, revealing an average genome completeness of 90.98% (SI Appendix, Table S6). Analysis of syntenic relationships, comparing genome assemblies of closely related species, also showed high continuity of these genomes (SI Appendix, Fig. S3).

Assembly statistics for the 17 novel marine mammal genomes generated for this study

We employed de novo and homology-based prediction methods to annotate the genes and repeat sequences of the assembled genomes (SI Appendix, Tables S7 and S8). Annotated protein-coding genes ranged from 20,083 to 20,947 per species (Table 1). The average gene lengths were similar to those of closely related species (SI Appendix, Fig. S4), and we recovered an average 96.44% of the BUSCO Mammalia gene set (4,104 genes) (Table 1). Overall, we generated high-quality genome sequences for 17 marine mammals, providing a good foundation for developing a better understanding of aquatic adaptation in marine mammals across three divergent ancestral lineages.

Combining published genome data with our 17 genomes, we were able to provide a detailed phylogenomic reconstruction of marine mammal species. Two nucleotide datasets were used (SI Appendix, Table S9): ortholog sequences from whole-genome alignment and reciprocal best hit ortholog genes from gene annotations. The maximum-likelihood trees generated from the alignments of the individual loci of the two datasets were used as input for the coalescent-based phylogenetic method ASTRAL-III (13), and these two datasets generated a consensus topology (SI Appendix, Fig. S5 and Fig. 1A). The overall phylogenetic relationship of three lineages of marine mammals is consistent with previous studies (8, 1416). For cetaceans, they support the monophyly of Physeteroidea + Kogiidae, Delphinidae, Monodontidae + Phocoenidae, and Ziphiidae among odontocete taxa, with Physeteroidea as the most basal clade of odontocetes, consistent with a recent large-scale phylogenomic analysis of cetaceans (17). For pinnipeds, there is support for a sister group relationship between Musteloidea and Pinnipedia and the monophyly of Odobenidae + Otariidae, consistent with studies based on mitochondrial DNA (18).

Phylogeny and population changes of marine mammals. (A) A maximum likelihood phylogenetic tree of 35 marine mammal species and 16 outgroup mammal species. Three lineages of marine mammals are distinguished by columns of different colors: Cetacea (blue), Pinnipedia (green), and Sirenia (red). Red stars represent the species differentiation node mentioned in the main text. (B) Population size history of three lineages of marine mammals. The normalized effective population size (Ne) of each species was estimated using pairwise sequentially Markovian coalescent. The Ne for each group of marine mammals is shown.

We further assessed divergence times for each marine mammal phylogenetic tree node (SI Appendix, Fig. S7). The divergence time between Cetacea and Hippopotamidae was estimated to be 55.5 Mya, which coincides with the PaleoceneEocene transition and a global temperature rise, which possibly prompted terrestrial mammals to enter the sea (19). The initial split of Mysticeti (baleen whales) and Odontoceti (toothed whales) was about 37.7 Mya. The emergence of Pinnipedia was estimated to be 27.4 Mya, while the divergence time between Odobenidae and Otariidae was about 18.6 Mya. The divergence time of sirenians and the African savanna elephant, their closest land relative, was estimated to be 63.9 Mya.

We also reconstructed the demographic histories of cetaceans, pinnipeds, and sirenians (SI Appendix, Table S10). The three marine mammal lineages were found to experience different historical changes in population size (see normalized average effective population size, Ne, in Fig. 1B and individual species profiles in SI Appendix, Fig. S8). Specifically, the Ne of cetaceans experienced a rapid decline during the last 500,000 y. Consistently, the heterozygosity rate of most cetaceans is even lower than the endangered giant panda [1.32 (20, 21)] (SI Appendix, Table S11), highlighting the ongoing conservation needs of cetacean species.

We compared the genome sizes of the three marine mammal lineages with their terrestrial relatives: Cetacea versus Ruminantia, Pinnipedia versus Canidae, and Sirenia versus Proboscidea. The average genome size of Pinnipedia (2.4 Gb) and Sirenia (3.1 Gb) was similar to their terrestrial sister taxa (Fig. 2B). In contrast, the genome size of cetaceans ranged from 2.4 to 2.6 Gb and displayed a decreasing trend compared to Ruminantia (2.8 Gb in reindeer, cattle, and goat), their most closely related lineage (Fig. 2B). Consistent with the genome size comparisons, pinnipeds and sirenians present similar repeat contents to their terrestrial sister taxa, while cetacean genomes have 10% fewer repeats than ruminants. Five subtypes of repeats are more abundant in ruminant species (SI Appendix, Table S12), including LINE/RTE-BovB, LTR/ERV1, LTR/ERVK, SINE/Core-RTE, and SINE/tRNA-Core-RTE. In addition to several reported large fragments in ruminant genomes (22), we found 11 large (>1.5 Mb) deletions and three large insertions (SI Appendix, Tables S13S15) in cetaceans, compared to their terrestrial counterpart cattle.

Structural characteristics and chromosome evolution of marine mammal genomes. (A) Circos plot of representative genomes of marine mammals: sperm whale, Indo-Pacific bottlenose dolphin (IPB dolphin), South American fur seal (SA fur seal), and spotted seal. (B) Genome sizes and transposable element content analysis of representative genomes of marine mammals. We selected three Ruminantia species, three cetacean species, three Canidae species, three pinniped species, an elephant, and a manatee. (C) Chromosome evolution of Cetacea and Pinnipedia. We reconstructed 23 and 19 ancestral chromosomes of Cetacea and Pinnipedia, respectively. The chromosome assignment to ancestral chromosomes is shown by colored bars, Indo-Pacific humpback dolphin (IPH dolphin).

Based on the eight chromosome-level genome assemblies that we generated (SI Appendix, Fig. S1) and two publicly available chromosome-level genomes [(sperm whale (23) and Indo-Pacific humpback dolphin (24)], we reconstructed the ancestral chromosomes of Cetacea (using the Indo-Pacific bottlenose dolphin as the reference genome) and Pinnipedia (using the South American sea lion as the reference genome) with DESCHRAMBLER (25) at 300-kb resolution (Fig. 2C). In Cetacea, we identified 1,308 conserved segments and reconstructed 23 ancestral predicted chromosome fragments (APCFs), with a total length of 2.09 Gb. In Pinnipedia, we identified 194 conserved segments and reconstructed 19 APCFs, with a total length of 1.84 Gb. We traced back the source of these APCFs for both lineages and found there are fewer chromosome rearrangement events in Pinnipedia than in Cetacea (Fig. 2C).

We next assessed the expansion and contraction of gene families, positively selected genes (PSGs), and rapidly evolving genes (REGs) in the three marine mammal lineages. In total, 44, 29, and 212 gene families were identified as expanded, and 87, 15, and 12 gene families were contracted in the ancestor node of Cetacea, Pinnipedia, and Sirenia, respectively (SI Appendix, Fig. S9). Functional enrichment analysis of these gene families revealed that olfactory transduction is the only shared contracted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway (SI Appendix, Table S16). Several expanded gene family-associated KEGG pathways are shared among two types of marine mammals: thermogenesis and oxidative phosphorylation in Cetacea and Pinnipedia and neural plasticity (as suggested by the alcoholism pathway) and estrogen signaling in Pinnipedia and Sirenia (SI Appendix, Table S17).

To assess the selective pressures acting on marine mammal genomes, we estimated the dN/dS ratio () using 7,252 orthologous, protein-coding genes. When compared with terrestrial outgroups, marine mammal branches always had a higher dN/dS ratio (SI Appendix, Fig. S10). We identified 5, 11, and 16 PSGs and 21, 17, and 295 REGs in the ancestral branches of Cetacea, Pinnipedia, and Sirenia, respectively (SI Appendix, Tables S18 and S19 and Fig. S9) (2 test, P < 0.05). We found that cystic fibrosis transmembrane conductance regulator (CFTR) underwent rapid evolution in both Pinnipedia and Sirenia. CFTR plays a vital role in the transport of various ions across the cell membrane, water transport, and fluid homeostasis (26, 27).

We identified 4,518,724 and 4,341,059 conserved noncoding elements (CNEs) in Cetacea and Pinnipedia, respectively. We further performed assay for transposase-accessible chromatin sequencing (ATAC-seq) (28) of two cetaceans (Indo-Pacific bottlenose dolphin and Rissos dolphin) and two pinnipeds (Baikal seal and South American sea lion) to identify CNEs associated with open chromatin (i.e., accessible to the transcriptional machinery). A total of 1,158 and 1,684 genes in Cetacea and Pinnipedia, respectively, have CNEs with ATAC-seq signal peaks within 3 kb upstream or downstream (SI Appendix, Tables S21 and 22). Of these genes, 371 have CNE peaks in both marine orders (SI Appendix, Table S23 and Fig. S11). Although further experimental work could be a worthwhile attempt to assess the contribution of these CNEs, our results provide a valuable resource for further studies on gene regulation in marine mammal species.

The evolution of marine mammals, the adaptation of terrestrial mammalian lineages to life histories dependent on the marine environment, is considered a seminal example of convergent evolution. The degree to which convergence is reflected at the molecular level can be addressed using genomics. Understanding this phenomenon addresses key questions about redundancy, pleiotropy, and the relationship between genotype and phenotype. We applied the Convergence at Conservative Sites method (29) to investigate convergent genes in the three lineages of marine mammals. Orthologous genes were assigned by synteny alignment (SI Appendix, SI Materials and Methods). We identified 195 convergent amino acid substitutions in 172 genes among marine mammals (SI Appendix, Tables S24). Only three genes (FAM20B, NFIA, and KYAT1) share convergent amino acid substitution in all three marine mammal lineages. Six genes (HERC1, MITF, EPG5, FAT1, SYNE1, and ATM) show convergent mutations at different amino acid positions in cetacean manatee and pinniped manatee. For example, MITF has an L10F substitution in cetaceans and sirenians (the manatee) and a T570A substitution in pinnipeds and the manatee. Among the 94 genes with convergent amino acid substitutions in the fully aquatic cetaceans and Sirenia, but not between the amphibious pinnipeds in either cetaceans or Sirenia, five genes are within the KEGG pathway dopaminergic synapse (though the adjusted P value is not significant at the 0.05 level: P = 0.51; SI Appendix, Table S25). Previous studies indicate that UCP1 has been independently lost in many marine mammals, especially in cetaceans and sirenians (30, 31). We confirm and extend this inference, showing that a functional UCP1 is present in most pinnipeds, except for the Antarctic fur seal, which is the most polar of the species included in this assessment (SI Appendix, Table S26 and Fig. S12).

Cetaceans have many unique biological characteristics, including echolocation, deep diving, and large variation in body size. The molecular basis of echolocation has been well studied previously (3234). However, based on more comprehensive data, we systematically reanalyzed the 504 hearing-related gene sequences in 40 species, including two groups of echolocating bats (group M: big brown bat, Natal long-fingered bat, Brandts bat, and little brown bat and group G: greater horseshoe bat) and 16 toothed whales (group T) (SI Appendix, Fig. S13). A total of 64 genes were identified as convergent genes, most reported in previous studies (SI Appendix, Table S27).

We next compared the four whale species with the best diving abilities to 20 comparatively shallow-diving species to study the genetic basis of deep diving in cetaceans. The deep-diving species are sperm whale (reported to dive to 1,860 m for >1 h) (35), Blainvilles beaked whale (1,251 m for 57 min) (36, 37), and dwarf and pygmy sperm whales [species in the family Kogiidae with highly similar ecology and habitat (up to 1,425 m for 43 min) (3840)]. We retrieved 1,803 genes from HypoxiaDB, a hypoxia-regulated protein database (41), and observed 39 genes with at least one specific amino acid change unique to the deep-diving group (SI Appendix, Table S28). MB encodes myoglobin, a protein critical for oxygen storage and transport (42). Deep-diving species have amino acid residue changes associated with elevated myoglobin net surface charge and maximal dive time (43). Compared with background branches, 45 genes showed significantly higher dN/dS ratios in deep-diving species (SI Appendix, Table S29) (2 test, P < 0.05). We detected 45 REGs in deep-diving cetaceans. Of these, three genes (SETX, GIF, and TMPRSS11D) had dN/dS values above 1, indicating positive selection. Seven REGs (CEP170, DHCR7, DSP, GBE1, PLD1, SETX, and TMPRSS11D) have shared amino acid mutations in the four deep-diving species.

Cetacean bodyweight spans orders of magnitude from 50 kg (the vaquita, Phocoena sinus) up to 180,000 kg (the blue whale, Balaenoptera musculus) (44). We selected a set of 1,528 genes involved in body size development and estimated their dN/dS ratios in cetaceans with large body size: the blue whale (3) and the sperm whale (3). Compared to the background, we found 102 REGs (with significantly higher dN/dS) in giant cetaceans (SI Appendix, Table S30 and Fig. S14) (2 test, P < 0.05). These REGs were enriched in the Hedgehog and Wnt signaling pathways essential for bone development (45) (SI Appendix, Table S31). Additional bone developmentrelated genes with a higher dN/dS in giant cetaceans include BMP1 in the TGF- signaling pathway and the Notch signaling pathway genes SNW1 and CTBP2.

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Comparative genomics provides insights into the aquatic adaptations of mammals - pnas.org

CRISPR/Cas9 platform announced the release of its transgene-free genome editing in plants to accelerate the research in the field of plant science for basic research.

New York, USA September 9, 2021 CRISPR/Cas9 platform, the professional division of Creative Biogene, focuses on providing comprehensive gene-editing services and products by using CRISPR/Cas9 technology. With professional products and services, CRISPR/Cas9 platform is dedicated to supporting the progress of gene editing projects. Recently, CRISPR/Cas9 platform announced the release of its transgene-free genome editing in plants to accelerate the research in the field of plant science for basic research.

CRISPR/Cas9 platform provides one-stop plant genome editing services, including gene knockout, gene knock-in and gene deletion. The service provides a variety of species, including but not limited to Arabidopsis, corn, rice, and tobacco. The specific workflow includes the design and construction of SgRNA, the delivery of Cas9 and sgRNA to plant cells, as well as targeted mutation analysis and final delivery.

CRISPR/Cas9 platform focuses on genome editing technology and provides comprehensive services to establish genome editing plants with specific genome engineering modifications on target genes/locus of interest. It also helps customers generate commercially viable target gene-edited crops, and produce non-GMO, non-regulated and sustainable genome-edited plants.

CRISPR/Cas9 platform provides GMO-free genome editing services for rice, tomato and Arabidopsis. Non-transgenic edited plants are generally obtained through genetic separation through selfing and crossing of T0 plants. Subsequently, PCR-based genotyping was used to identify T1 plants without DNA. CRISPR/Cas9 Platform also provides other strategies, such as RNP/RNA-based methods and marker-assisted transgene elimination to meet specific requirements.

CRISPR/Cas9 platform has been committed to improving plant transformation efficiency and optimizing genome editing systems for many years. Two different base editors have recently been introduced, Cytosine Base Editor (CBE) and Adenine Base Editor (ABE). CBE realizes the efficient substitution of CG to TA, and ABE mediates the transformation of AT to GC in genomic DNA. CRISPR/Cas9 Platform combines a base editor with genetic transformation technology to generate single base substitutions in the plant genome. It has been applied to precision plant breeding and transformation in agriculture.

With excellent experts and years of plant genome editing experience, we provide global customers with one-stop services from project design to genetically modified plant screening. said Marcia Brady, the marketing director of Creative Biogene, she also added, Also, we are committed to offering customized solutions to satisfy specific needs, providing professional consultation and evaluation for specific projects.

About CRISPR/Cas9 platform

CRISPR/Cas9 platform, as a professional division of Creative Biogene, is dedicated to supporting our clients conduct genetic research with comprehensive gene-editing services and products as well as experienced in-house experts. With years of effort. Creative Biogene CRISPR/Cas9 platform has become a world-recognized industry platform that supports millions of scientists worldwide.

Media ContactCompany Name: Creative BiogeneContact Person: Marcia BradyEmail: Send EmailPhone: 1-631-386-8241Country: United StatesWebsite: https://www.creative-biogene.com/crispr-cas9

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CRISPR Cas9 Platform Provides One-stop Transgene-Free Genome Editing in Plants to Support the Research of Plant Science - Digital Journal

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The rest is here:
Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |...

Significance

Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated genomic resources for Hawaiian Metrosiderosa hyper-variable adaptive radiation of woody taxafor insights into the paradox of remote island radiations. We posit that divergent selection and differential sorting of an unexpectedly rich pool of ancestral variation drove the diversification of lineages. Recurring use of ancient variants from a richer-than-expected gene pool may explain how lineages can diversify to fill countless niches on remote islands.

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.

Adaptive radiations exhibit extraordinary levels of morphological and ecological diversity (1). Although definitions of adaptive radiation vary (27), all center on ecological opportunity as a driver of adaptation and, ultimately, diversification (2, 810). Divergent selection, the primary mechanism underlying adaptive radiations, favors extreme phenotypes (11) and selects alleles that confer adaptation to unoccupied or under-utilized ecological niches. Differential adaptation results in divergence and, ultimately, reproductive isolation between populations (12). Adaptive radiations demonstrate the remarkable power of natural selection as a driver of biological diversity and provide excellent systems for studying evolutionary processes involved in diversification and speciation (13).

Adaptive radiations on remote oceanic islands are especially interesting, as colonization of remote islands is expected to involve population bottlenecks that restrict genetic variation (14). Adaptive radiations in such settings are especially impressive and even paradoxical, given the generation of high species richness from an initially limited gene pool (15). Several classic examples of adaptive radiation occur on oceanic islands, such as Darwins finches from the Galapagos islands (16), anole lizards from the Caribbean islands (9), Hawaiian Drosophilids (17), and Hawaiian silverswords (18), to name a few.

Recent advances in genome sequencing and analyses have greatly improved our ability to examine the genetics of speciation and adaptive radiation. By examining sequences of multiple individuals from their natural environment, it has become possible to catch in the act the speciation processes between incipient lineages (19). Genomic studies of early stage speciation show that differentiation accumulates in genomic regions that restrict the homogenizing effects of gene flow between incipient species (20). The number, size, and distribution of these genomic regions can shed light on evolutionary factors involved in speciation (19). Regions of high genomic differentiation can also form from evolutionary factors unrelated to speciation, such as linkage associated with recurrent background selection or selective sweeps on shared genomic features (21, 22).

Genomic studies of lineages undergoing rapid ecological diversification have begun to reveal the evolutionary mechanisms underlying adaptive radiations. Importantly, these studies highlight the pivotal role of hybridization between populations and the consequent exchange of adaptive alleles that facilitates rapid speciation and the colonization of diverse niches (2325). Most genomic studies of adaptive radiation involve animal systems, however, in particular, birds and fishes. In plants, genomic studies of adaptive radiation are sparse (2628), and all examine continent-wide radiations. There are no genomics studies of plant adaptive radiations in geographically restricted systems such as remote islands. Because the eco-evolutionary scenarios associated with adaptive radiations are diverse (5, 29), whether commonalities identified in adaptive radiations in animals (23, 30) are applicable to plants is an open question. For example, the genetic architecture of animal adaptive radiations typically involves differentiation at a small number of genomic regions (3133). In contrast, the limited insights available for plants suggest a more complex genetic architecture (26).

We investigated the evolutionary genomics of adaptive radiation in Metrosideros Banks ex Gaertn. (Myrtaceae) across the Hawaiian Islands. Hawaiian Metrosideros is a landscape-dominant, hypervariable, and highly dispersible group of long-lived (possibly >650 y) (34) woody taxa that are nonrandomly distributed across Hawaiis heterogeneous landscape, including cooled lava flows, wet forests and bogs, subalpine zones, and riparian zones (35, 36). About 25 taxa or morphotypes are distinguished by vegetative characters ranging from prostate plants that flower a few centimeters above ground to 30-m-tall trees, and leaves range dramatically in size, shape, pubescence, color, and rugosity (35, 37, 38); a majority of these forms are intraspecific varieties or races (provisional varieties) of the abundant species, Metrosideros polymorpha (35, 36, 38). Variation in leaf mass per area within the four Metrosideros taxa on Hawaii Island alone matches that observed for woody species globally (39). Common garden experiments (38, 4044) and parentoffspring analysis (45) demonstrate heritability of taxon-diagnostic vegetative traits, indicating that taxa are distinct genetic groups and not the result of phenotypic plasticity. Metrosideros taxa display evidence of local adaptation to contrasting environments (46, 47), suggesting ecological divergent selection is responsible for diversification within the group (48). This diversification, which spans the past 3.1 to 3.9 million years (49, 50), has occurred despite the groups high capacity for gene flow by way of showy bird-pollinated flowers and tiny wind-dispersed seeds (36, 51). Lastly, the presence of partial reproductive isolating barriers between taxa is consistent with the early stages of speciation (52). Here, we generated several genomic resources for Hawaiian Metrosideros and used these in population genomics analyses to gain deeper insights into the genomic architecture and evolutionary processes underlying this island adaptive radiation.

Using nanopore sequencing, an individual of Metrosideros polymorpha var. incana was sequenced to 66 coverage (refer to SI Appendix, Table S1 for genome-sequencing statistics). The reads were assembled into a draft assembly that had high contiguity with a contig N50 of 1.85 M basepair (bp) (Table 1). We implemented Pore-C sequencing (53), which combines chromosome conformation capture with long-read nanopore sequencing, to assay the Metrosideros-specific chromosome contact map and anchor contigs to their chromosomal positions (refer to SI Appendix, Table S2 for Pore-C sequencing statistics) (54). Using Pore-C contact maps, initial assembly contigs were scaffolded into 11 superscaffolds (Fig. 1A) spanning 292.8 Mbps with an N50 of 25.9 Mbp. Compared to a previous genome assembly that was based only on Illumina sequencing (55), our assembly was similar in total genome size but had significantly higher contiguity. The number of superscaffolds was consistent with the 11 chromosomes in Metrosideros (56). The assembly was evaluated with 2,326 Benchmarking Universal Single-Copy Ortholog (BUSCO) genes from eudicots, and 2,183 genes (93.8%) were present. These results suggest that our chromosome-level genome assembly is highly contiguous and complete. Gene annotation was conducted using nanopore sequencing of a complementary DNA (cDNA) library generated from leaf tissue (refer to SI Appendix, Table S3 for cDNA sequencing statistics). A total of 28,270 genes were predicted with 94.2% of the transcripts showing an annotation edit distance of less than 0.5.

Genome assembly statistics for M. polymorpha var. incana

Genomics of Hawaiian Metrosideros. (A) Pore-Cbased chromosome contact matrix for M. polymorpha var. incana. Black boxes indicate the 11 superscaffolds (pseudochromosomes). (B) Geographic distribution and taxon classification for the 135 samples that were analyzed in this study. Numbers in parentheses represent sample sizes. (C) PCA and individuals are color coded according to B. (D) Ancestry proportion estimates using the ADMIXTURE algorithm for K = 3, 7, and 14. Taxa/populations are separated by dotted lines and colors above admixture barplots represent taxa as in B while taxon names are labeled below.

We investigated the population genomics of Hawaiian Metrosideros by whole-genome resequencing 89 individuals from the islands of Oahu and Kauai and combining these data with previously published sequence data from Hawaii Island and Molokai (57). Our sampling from the Maui Nui complex (e.g., Molokai) included just a few samples, as past studies have shown a mixed ancestry for Metrosideros on Maui Nui involving colonization from both older and younger islands (35, 49), and our evolutionary analyses were centered on island-endemic communities. We also sequenced three Metrosideros species outside of Hawaii for use as outgroup genomes (one Metrosideros excelsa from New Zealand, one Metrosideros robusta from New Zealand, and two Metrosideros vitiensis from American Samoa and Fiji). In total, we analyzed 131 individuals belonging to 11 Hawaiian taxa, abbreviated as: M. polymorpha race B (B), M. polymorpha race C (C), M. polymorpha race F (F), M. polymorpha race L (L), M. polymorpha var. glaberrima (G), M. polymorpha var. incana (I), M. macropus (M), M. polymorpha var. newellii (N), M. rugosa (R), M. tremuloides (T), and M. polymorpha var. waialealae (WW) (Fig. 1B).

A total 10 of the Hawaiian taxa are single-island endemics (i.e., B, C, F, L, M, N, R, T, and WW) or have multi-island distributions but are sampled from just one island (i.e., I) and are thus described here as taxa because each of these taxa is represented in this study by a single sampled population. The 11th taxon, archipelago-wide G, is represented by three populations from three islands, which are thus described as populations. The median genome coverage was 14 per individual, and on average, 93% of the sequencing reads were aligned to our reference genome (SI Appendix, Table S4). The mapped reads were used to call single nucleotide polymorphisms (SNPs), and after filtering, there were 22,511,205 variable sites that were used for subsequent analysis.

Using the population genomics data, we investigated the genetic structure across Hawaiian Metrosideros through principal component analysis (PCA) and ancestry analysis. PCA separated the taxa/populations by island of origin, and within islands, individuals were largely clustered by taxon (Fig. 1C). Finer scale evolutionary relationships were examined by estimating genomic ancestry proportions (K) for each individual (refer to SI Appendix, Fig. S1 for K = 3 to K = 15 results). Consistent with the PCA results, at low K, ancestries strongly reflected island of origin (Fig. 1D). With increasing K, each taxon/population showed increasingly unique ancestry, and at K = 14, with few exceptions, individuals belonging to the same taxon/population shared a single, unique ancestry. The exceptions were F and I, for which a majority of the individuals showed admixed ancestries. On Hawaii Island, G belonged to two genetic groups designated GH1 and GH2 in our previous analysis, and GH2 represented a recently admixed population with N (57). At least some individuals of F and I on Oahu and GH2 on Hawaii Island were likely to be hybrids formed from recent hybridization of genetically distinct populations (58).

We inferred the evolutionary relationships among taxa by building a maximum-likelihood phylogenomic tree using genome-wide, fourfold-degenerate sites (Fig. 2A) and M. vitiensis as the outgroup. The internal branch lengths of all Hawaiian Metrosideros were short, consistent with a rapid radiation within the islands (Fig. 2A, Left). Differentiation among taxa was relatively low, with pairwise FST values ranging from 0.002 between C and I to 0.16 between M and GK (SI Appendix, Fig. S2). Collapsing the branch lengths to view the topological relationships revealed that individuals grouped by island with little evidence of recent migration between islands (Fig. 2A, Right). Within the phylogeny, individuals clustered according to taxon/population classification and were monophyletic with high confidence (>95% bootstrap support). Exceptions were the paraphyletic relationships among the pubescent Oahu taxa (C, F, I, and R) and between G and N on Hawaii Island. For the Oahu taxa, there was strong phylogenetic grouping for the glabrous pair B and L and for the glabrous pair M and T, but the topological relationships between these glabrous subgroups and within the pubescent group were unresolved. We used SNP and AFLP package for phylogenetic analysis (SNAPP) (59) as an independent Bayesian phylogenetic method to infer the multilocus phylogenetic trees and the uncertainty in the majority-rule topology. The SNAPP cloudogram showed a single major topology that was consistent with the maximum-likelihood tree topology (SI Appendix, Fig. S3) with the exception of the four glabrous taxa from Oahu, which showed contrasting relationships in the two trees.

Divergence time and demographic history of Hawaiian Metrosideros. Relative times were converted to absolute times assuming a mutation rate of 7 109 mutations per base pair per generation and a 20-y generation time. (A) Genome-wide maximum-likelihood tree built using fourfold degenerate sites. A tree with branch lengths is shown on left and a tree without branch lengths but showing phylogenetic relationships with bootstrap is on Right. Outer circle colors indicate island of origin for each sample, and inner circle colors indicate taxa as in Fig. 1B. All Hawaiian Metrosideros taxa have glabrous (hairless) leaves, except the four Oahu pubescent taxa indicated in the outer-most ring of Left tree. The four Oahu glabrous taxa are also highlighted in outer-most ring of Right tree. Nodes with greater than 95% bootstrap support are indicated with blue circles in Right. (B) G-PhoCS-estimated divergence times for representative taxa/populations GH1 (M. polymorpha var. glaberrima from Hawaii), GM (M. polymorpha var. glaberrima from Molokai), M (M. macropus from Oahu), and GK (M. polymorpha var. glaberrima from Kauai) (Above) and time of geological formation of each island based on Clague (102) (Below). Tree is rooted with outgroup M. vitiensis (Mv). (C) MSMC2-estimated effective population size for each Hawaiian taxon, color-coded as in Fig. 1B.

Results from the analysis of evolutionary relationships suggested a reticulate evolution for Hawaiian Metrosideros, which we investigated further using Pattersons D-statistics (ABBA-BABA D test) (60, 61). Specifically, we looked for evidence of hybridization between taxa by calculating Pattersons D-statistics for all population trios following the radiation-wide topology (Fig. 2A). M. vitiensis was used as the outgroup, specifically the sample from Fiji due to its high genome coverage. Overall, 85 of the 159 (53.5%) trio topologies had significant D-statistics (Bonferroni corrected P value < 0.05; refer to SI Appendix, Fig. S4 for results of each trio), indicating hybridization. Of the 85 trios, 53 (62.4%) topologies involved admixture between taxa on different islands, indicating that reticulate evolution was pervasive within and between islands. The relatively strongly isolated M and T were exceptions, as they had the fewest significant D-statistics and no evidence of admixture with lineages outside of Oahu (SI Appendix, Fig. S4).

Because the topological support values within the glabrous and pubescent Oahu groups were low (Fig. 2A) and indicating uncertain relationships, we examined patterns of discordance in the phylogenetic signal across the genome using TWISST (62). For a rooted four-taxon tree, there are 15 possible topologies, and we used TWISST to estimate the weight (frequency) of each topology in 10-kbp windows across the genome. Results from TWISST showed no single, dominant topology highly represented across the genome, and the difference in weight between the most common and second most common topologies was just 1.5% (SI Appendix, Fig. S5) for both the glabrous and pubescent groups. Simulations indicated a large ancestral effective population size (i.e., high incomplete lineage sorting) (63) for both groups, and admixture between ancestral populations could explain the topological weights observed for the Oahu taxa (SI Appendix, Fig. S6).

We next examined the topological weights (frequencies) across the Hawaiian Islands, but using just GH1, M, and GK to represent Hawaii, Oahu, and Kauai, respectively, as these taxa/populations showed no evidence of admixture with each other (SI Appendix, Fig. S4). Results showed that the topology with the highest weight was consistent with the topology generated for all taxa (Fig. 2A), but the weight of this topology was only 10% higher than the weights of the two alternative topologies (SI Appendix, Fig. S7). Combined, these results indicated a highly reticulated evolutionary history for Hawaiian Metrosideros, part of which was largely driven by elevated levels of shared ancestral polymorphisms that have not sorted completely among taxa.

We investigated the speciation history of Hawaiian Metrosideros through demographic modeling. The population divergence times were estimated using the generalized phylogenetic coalescent sampler (G-PhoCS) (64). Because we were interested in the colonization history of Metrosideros across the islands, we chose a single individual to represent each island. Specifically, we chose a single individual of G from each of Hawaii, Molokai and Kauai, and a single individual M from Oahu, because G samples from Oahu were not available. M showed no significant evidence of between-island admixture (SI Appendix, Fig. S4), which reduced the number of admixture models to be tested with G-PhoCS.

Initially, we ran G-PhoCS models fitting migration bands (i.e., admixture) between populations. Results showed that including admixture had no effect on estimates of divergence times (SI Appendix, Fig. S8). Given this result, we based our divergence-time analysis on the simple no-migration model. The G-PhoCS-estimated divergence time between Hawaiian Metrosideros and the outgroup, M. vitiensis, was 4.36 million years ago (MYA) (95% Highest Posterior Density 4.16 to 4.55 MYA). We also examined the effect of changing the mutation rate and generation time on absolute divergence time estimates. Using the range of mutation rates observed in plants [i.e., 7 109 in Arabidopsis (65) to 9.5 109 in Prunus (66)] and a higher generation time of 25 y, a conservative divergence time estimate for Hawaiian Metrosideros and M. vitiensis was 4 to 5.5 MYA (SI Appendix, Fig. S9). These estimates encompass the estimated timing of the subaerial appearance of Hawaiis oldest main island, Kauai (Fig. 2B). Given that M. vitiensis is not the most closely related outgroup species to Hawaiian Metrosideros (50), however, colonization of the Hawaiian Islands likely occurred more recently than 4.36 MYA. Within the Hawaiian Islands, divergence time estimates were consistent with colonization of each island following its formation. The exception was Hawaii Island for which the divergence time of Metrosideros predated the geological formation of that island, consistent with the results of our previous study (57).

We also estimated past changes in effective population size (Ne) for each taxon/population using the program Multiple Sequentially Markovian Coalescent 2 (MSMC2) (67, 68). From each taxon/population, we chose a single individual for analysis. Results showed that all taxa had identical trajectories that included a decrease in Ne until 3 MYA, followed by an increase and subsequent drop in Ne in a pattern unique to each taxon (Fig. 2C). This result suggested that all Hawaiian Metrosideros taxa share the same common ancestor that experienced a population bottleneck 3 to 4 MYA, which is likely when the ancestral population initially colonized the islands. Based on G-PhoCS and MSMC2 analyses, the initial colonization of the Hawaiian Islands was estimated at 3 to 4.4 MYA (150,000 to 220,000 generations ago).

To investigate the genetic architecture underlying the Metrosideros radiation we narrowed our analysis to pairs of taxa/populations that were phylogenetic sisters (pair GH1 and N, pair C and R, pair M and T, and pair B and L), since for these sister pairs, the pattern of genome-wide differentiation reflects relatively recent divergence. We used MSMC2 to estimate the relative cross-coalescence rate (67) and population separation time for each sister pair (SI Appendix, Fig. S10). The relative cross-coalescence rates indicated the four sister pairs had comparable split times (GH1 versus N 635 KYA, C versus R 612 KYA, M versus T 693 KYA, and B versus L 888 KYA). For each sister pair, we used ai (69) to fit 20 different demographic models (refer to SI Appendix, Table S5 for complete ai results and SI Appendix, Fig. S11 for visualization of all models) to find the best-fitting model to explain its divergence history. Results showed that pair GH1 and N and pair C and R were consistent with a speciation model in which divergence occurred with continuous gene flow (i.e., primary gene flow) (70), while in pair B and L and pair M and T, the populations have been largely isolated from each other with the exception of either a recent or ancient gene flow event (Fig. 3A).

Genomic landscape of differentiation for the four phylogenetic sister pairs. (A) Best-fitting demography model based on ai modeling. (B) Genome-wide FST in 10-kbp windows. Yellow dots are outliers identified with z-scoretransformed FST values (zFST) > 4.

We investigated the genomic architecture of the Metrosideros adaptive radiation by quantifying genome-wide patterns of differentiation and signatures of divergent selection between sister taxa. We focused on differentiation (FST) outlier regions since these regions would harbor genetic variation associated with the divergence of sister pairs (71). Results showed that, in all four sister pairs, areas of high genomic differentiation were scattered across all 11 chromosomes (Fig. 3B). Pair M and T had the fewest outlier windows (52 zFST outlier windows), while pairs GH1 and N, C and R, and B and L had over 250 zFST outlier windows each (257, 269, and 260, respectively). The median genome-wide FST between M and T (FST = 0.16) was more than twice the level of FST within the other sister pairs (GH1 and N median FST = 0.04; C and R median FST = 0.04; B and L median FST = 0.07), suggesting that increased genome-wide differentiation between M and T due to their genetic isolation may have eroded outlier windows to undetectable levels (26, 72). The genomic positions of outlier windows generally did not overlap across the four sister pairs (i.e., >84% of outlier windows were found in only one pair; SI Appendix, Fig. S12).

Because genomic outliers of differentiation do not always result from divergent selection (7375) and FST may be a biased estimate of differentiation (76), we also examined levels of absolute genetic divergence (Dxy) within differentiation outlier regions. Dxy is expected to be elevated in genomic regions under divergent selection or regions acting as barriers between populations (73). Within each sister pair, Dxy levels were significantly elevated in differentiation outliers (MannWhitney U test P value < 0.001) relative to the genomic background (Fig. 4A). The differentiation outliers were also significantly elevated for values of relative node depth (21, 77) (SI Appendix, Fig. S13), which corrects for differences in mutation rate among loci by dividing Dxy values by the average Dxy to an outgroup (here, M. vitiensis). Differentiation outliers also had significantly lower levels of polymorphism and significantly higher values for selective sweep statistics, compared to the genomic background (SI Appendix, Fig. S14). These indicated that heterogeneity in mutation rate was not responsible for elevated Dxy in the differentiation outliers. In addition, the density of repetitive elements did not differ between the differentiation outliers and the genomic background (SI Appendix, Fig. S15), suggesting that elevated Dxy was not an artifact of misaligned and erroneous genotype calls. Instead, the differentiation outlier regions formed between Metrosideros sister taxa appear to have arisen through divergent selection.

Population genetics of the differentiation (FST) outlier regions identified in sister pairs. (A) Sequence divergence (Dxy) statistics calculated in 10-kbp windows. Red boxes are statistics from the genomic background, and green boxes are statistics from the differentiation outlier regions. (B) Localized admixture statistics (fdM) calculated in 10-kbp windows for the differentiation outlier regions identified in sister pairs (A). fdM is a rooted four-population statistic, in which P1 and P2 represent sister taxa and a positive fdM statistic indicates admixture between a third lineage, P3, and P2; while a negative fdM statistic indicates admixture between P3 and P1. For fdM, the genome-wide background is not shown to highlight the differentiation outlier region fdM values. Shown are values for median, first, and third quartiles, with whiskers representing 1.5* interquartile range. * indicates P < 0.001 after MannWhitney U test comparing differentiation outlier region versus the genomic background.

A gene ontology (GO) enrichment analysis was done to identify any overrepresented functional categories associated with the differentiation outlier regions. Results showed that genes within the outlier windows were enriched for 19 GO terms in the biological process category with functions largely related to metabolic processes, cell cycle, and diseaseimmunity responses (SI Appendix, Fig. S16).

We focused next on the evolutionary origin and history of the differentiation outlier regions as they relate directly to the genetic basis of the Hawaiian Metrosideros radiation. Due to the highly reticulated evolutionary history of Hawaiian Metrosideros, we initially examined differentiation outliers in the sister pairs for evidence of admixture from a nonsister taxon. Specifically, we asked whether the differentiation outliers that formed between the two sister taxa have evolutionary origins from a nonsister taxon. This would emphasize the importance of recent introgression from more distantly related taxa in forming the differentiation outliers observed between sister pairs (70). We calculated the fdM statistic (32), which quantifies admixture within genomic windows between both members of a sister pair and a third lineage. Results showed the Hawaii Island pair GH1 and N was the only sister pair in which the fdM statistics did not differ between the differentiation outliers and the genomic background (Fig. 4B). For each of the three other sister pairs (all on Oahu), the differentiation outliers had significant evidence of admixture with another Oahu taxon, while the pair C and R showed significant evidence of admixture with Hawaii Island taxa as well. These results suggested that hybridization from a more distantly related taxon may have contributed to the genomic regions that are significantly diverged between sister taxa in Metrosideros.

We further examined the possible role of recent introgression from nonsister taxa in the formation of differentiation outliers between sister taxa using phylogenetic analysis. Initially, the evolutionary histories of the differentiation outliers were visualized by concatenating the outlier regions and building a maximum-likelihood phylogenetic tree for each sister pair (SI Appendix, Fig. S17). In each case, the phylogenetic tree of the differentiation outliers was similar in its structure to the genome-wide phylogeny. Individuals were largely monophyletic by taxon/population in each phylogeny, and with the exception of the sister pair, the topological relationships were consistent with the genome-wide topology (Fig. 2A). For all four sister pairs, one taxon (i.e., GH1, L, R, and T) was topologically discordant (SI Appendix, Fig. S17 red star) compared to the genome-wide topology. The cause of this discordance (i.e., the evolutionary origin of the outlier regions) was uncertain due to the low phylogenetic support, and the low phylogenetic support was not due to introgression according to the fdM statistics (Fig. 4B). Moreover, with a single exception (i.e., C compared with I), these regions had significantly elevated Dxy levels in pairwise comparisons with all other Hawaiian taxa (SI Appendix, Fig. S18). Combined, these results suggested that the elevated Dxy observed in differentiation outliers between sister taxa was in fact not due to recent introgression from outside the sister pair.

To further investigate the evolutionary origins of the differentiation outlier regions, we followed a recently developed approach that examines allele states in related populations to characterize the evolutionary history of polymorphisms in a focal group (78, 79). Specifically, for each sister pair individually, we pulled out sites that were polymorphic within the pair and determined the allele states for each within taxa or populations on other islands. This analysis divided the polymorphic sites in each sister pair into three classes that are interpreted as follows (refer to Fig. 5, Top for visual representation of the classes) 1): Sites with variants that are private to the sister pair. Such variants are likely to be young and possibly unique to the island hosting the sister pair (but see class-1a below) 2); Sites that are polymorphic within taxa/populations on two or all three of the islands examined. Such sites represent shared (unsorted) ancestral polymorphisms; and 3) Sites at which two taxa/populations from two other islands (i.e., islands not hosting the sister pair) are fixed for alternative alleles. Such sites are polymorphic in the sister pair as a result of between-island hybridization, or they represent alleles with negative epistatic interactions (i.e., Bateson-Dobzhansky-Muller incompatibilities) in the ancestral population. These three classes represent mutually exclusive categories of polymorphic sites in the sister pairs. Lastly, to allow detection of polymorphisms that may predate the initial colonization of the islands, we pulled out a subclass of class-1 sites (class-1a). Class-1a sites are sites at which the two taxa/populations from the different islands are fixed for the same allele and the outgroup M. vitiensis is fixed for the alternative allele. Given that the differentiation outliers in the sister pairs have elevated Dxy in all pairwise comparisons within the Hawaiian radiation (SI Appendix, Fig. S18), such sites are likely to represent variants that predate the Hawaiian radiation.

Evolutionary origins of the genome-wide SNPs and the differentiation (FST) outlier-region SNPs between the sister taxa, GH1 and N. The Top figure illustrates the allele state in taxa outside of Hawaii Island for a site that is polymorphic across the sister pair GH1 and N and four possible evolutionary scenarios (classes) that can result in the polymorphism. The Bottom figure shows the proportion of variants identified within the GH1-N differentiation outlier regions that are designated to each class. Numbers within the bars represent the total number of genome-wide SNPs that fall within each class. *** indicates P < 0.001 after Fishers exact test.

We first categorized the genome-wide polymorphisms segregating within the Hawaii Island pair GH1 and N according to allele states in M from Oahu and GK from Kauai (Fig. 5, Bottom). A majority of the GH1-N polymorphisms were categorized as class-1 (i.e., private to GH1-N) (3,268,871 SNPs). A large proportion of the polymorphic sites, however, was classified as class-2 (2,268,930 SNPs), consistent with our previous analysis that revealed extensive sharing of ancestral polymorphisms across the Hawaiian radiation. We then narrowed the analysis to just the subset of polymorphic sites that occurred within the differentiation outlier regions to test whether they were enriched for a specific class. Results showed significantly greater enrichment of class-3 sites relative to the other three classes (Fishers exact test P value < 0.0001). Because there was no significant evidence of between-island admixture among the four populations examined (i.e., GH1, N, M, and GK) and because the fdM statistics revealed no evidence of admixture within the differentiation outlier regions for GH1 and N, the enrichment of class-3 sites within differentiation outliers is likely due to the sorting of ancestral incompatibility alleles. Further, the GH1-N differentiation outliers were significantly more enriched for class-2 and class-1a sites compared to class-1 sites (Fishers exact test P value < 0.0001), providing further support for the importance of ancestral polymorphisms in the formation of differentiation outliers. We applied this analysis to the three Oahu sister pairs next and again found significant enrichment of class-3 sites in the differentiation outliers (Fishers exact test P value < 0.0001; SI Appendix, Fig. S19). Since recent introgression is insufficient to explain the increased Dxy in the differentiation outliers (SI Appendix, Figs. S17 and S18), these results indicate a strong role for the sorting of ancestral incompatibility alleles in the formation of differentiation outliers in all four sister pairs examined.

How lineages are able to undergo rapid phenotypic and ecological diversification in isolated ecosystems is a perplexing question in evolutionary biology (15). The limited genetic variation in the founding populations that give rise to such radiations and the relatively slow rate of genetic mutation (80) are expected to restrict speciation rates in remote settings. Plant adaptive radiations on islands have been studied largely through phylogenetic approaches using DNA sequences or genomes of a single representative from each species within the radiation (81, 82). These phylogenetic analyses of island plant groups have addressed questions of monophyly and revealed significant insights into the patterns and timing of island colonization and trait evolution. We took an alternative approach to investigate the evolution of Hawaiis landscape-dominant woody genus, Metrosideros, by constructing a chromosome-level genome assembly and sampling genome-wide variation of 131 individuals across the islands. Using a population genomics approach, we gained deeper insights into the evolutionary history of the Hawaiian Metrosideros radiation, including the demographic processes and genomic architecture underlying this island adaptive radiation. Our findings suggest that diversification of Hawaiian Metrosideros was facilitated by reassortment of an unexpectedly rich pool of ancestral polymorphisms.

Several adaptive radiations have been shown to be facilitated by the reuse of genetic variants that are older than the radiations themselves (23, 25), a recurring observation that demonstrates the evolutionary importance of standing genetic variation for adaptive radiation (83). One way that an enriched pool of standing variation can become established in an isolated setting is through colonization by an ancestor of hybrid origin (25). The hybrid-swarm origin of adaptive radiation model proposes that such hybrid populations are predisposed to adaptive radiation (24, 84) by 1) providing novel characters through transgressive segregation (85) and 2) breaking genetic correlations that constrain trait evolution (86). Ancient hybrid origins have been suggested for a number of adaptive radiations, in particular in fish systems such as the Alpine whitefish (87) and the East African cichlids (78, 79, 88). In plants, adaptive radiations of the allopolyploid silverswords (82) and endemic mints (89) of Hawaii are also thought to have originated from ancient hybridizations. In cases of adaptive radiation through polyploidization, however, it is not certain how much of the radiation can be attributed to the duplication of functional genetic elements (90) or to the ploidy increase itself (91).

Hawaiian Metrosideros may also have a hybrid origin. Incomplete sorting of the considerable ancestral polymorphism created through hybridization could explain the highly reticulate evolution seen within the group. A large pool of ancestral variants would have served as readily available genetic variation for adaptation, without the waiting times required for de novo adaptive mutations. Indeed, we discovered that genomic divergence (and potentially the genetic basis of reproductive isolation) between early diverging Metrosideros taxa was shaped by divergent selection targeting ancestral variations over evolutionary young de novo variations. Interestingly, the highest proportion of ancestral variations occurring within the differentiation outlier regions comprised those that were fixed for alternative alleles in other taxa from different islands and thus may have had negative epistatic interactions in the ancestral population. Differential sorting of these ancestral incompatibility alleles has been proposed as a mechanism of reproductive isolation between hybrid lineages (92), and this may have facilitated genetic divergence and the evolution of the intrinsic, postzygotic isolating barriers that have been observed within Hawaiian Metrosideros (52).

Alternatively, the patterns we observe could be explained by initial colonization of the Hawaiian Islands by a sizable population of mixed or panmictic ancestry. This scenario appears less probable, however, given that Metrosideros likely colonized the Hawaiian Islands from the Marquesas Islands south of the equator (50, 93, 94), which required traversing more than 3,000 km of open ocean against the prevailing low-altitude trade winds (94). Metrosideros in the Marquesas Islands comprises just a single extant species (Metrosideros collina) with no recognized subspecific taxa. Moreover, genetic variation within the Marquesan Metrosideros population is expected to be limited as a result of the serial founder events associated with the colonization of the more remote Pacific Islands from the south Pacific (93, 94). If in fact Hawaiian Metrosideros descends from a true founder event from the Marquesas Islands, this would suggest that the striking adaptive radiation of Metrosideros observed in Hawaii but not in other remote Pacific Island chains results simply from the greater ecological opportunity in Hawaii. The main Hawaiian Islands have the largest current and historical geographic areas, elevation, and environmental heterogeneity of any island chain in the remote Pacific (95, 96). Further genome-wide studies of this genus throughout the Pacific region will be required to uncover the sources of ancestral genetic variation in Hawaiian Metrosideros.

In both animals and plants, adaptive evolution fuels the diversification of species, but the nature of the traits under selection can lead to fundamental differences in the genomic architecture of adaptive radiation. The genome-wide distribution of differentiation outliers in this study suggests that ecological diversification within Metrosideros involves either a large number of traits of simple genetic architecture or fewer traits with a polygenic basis (97, 98), with the latter being a more likely explanation for the rich diversity of vegetative traits in the group. These patterns contrast with the genetic architecture observed for key traits in animal adaptive radiations, in which differentiation is seemingly localized to a few genomic regions with prominent, broad peaks (3133). In animals, traits under ecological selection can often cause physical changes that ultimately become involved in mate choice and assortative mating by sexual selection (99, 100). In Metrosideros, the outlier peaks were narrow, and their distribution was heterogeneous across the genome, a pattern that was also found in the continent-wide adaptive radiation of sunflowers (26). The narrow peaks suggest that fine-scale mapping of the genes underlying divergent phenotypes may be possible.

Detailed description of materials and methods can be found in SI Appendix. Briefly, we generated a reference de novo genome assembly for Metrosideros using the Oxford Nanopore Technologies GridION sequencing platform. An M. polymorpha var. incana (NG4) was genome-sequenced, assembled using flye (101), and scaffolded using Pore-C sequencing (53). For population genomic analysis, we genome-sequenced 92 samples and combined with our previous population genomic sampling (57). Sequencing reads were aligned to the reference genome that was generated from this study, and the genome-wide variations were analyzed for determining the population relationship, demographic history, and the population genomics of the Hawaii Metrosideros adaptive radiation.

Nanopore sequencing data are available from National Center for Biotechnology Information (NCBI) bioproject ID PRJNA670777. The population genomic sequencing data are available from NCBI bioproject ID PRJNA534153, specifically with the Sequence Read Archive Run (SRR) identifiers SRR12673403 to SRR12673495. Data generated from this study, including the reference genome assembly, gene annotation, variant call file, and population genetics statistics can be found at Zenodo data repository (https://doi.org/10.5281/zenodo.4264399).

We thank the Hawaii Division of Forestry and Wildlife for permission to collect leaf samples from state forests. We also thank Jennifer Johansen, Yohan Pillon, Melissa Johnson, and Chrissen Gemmill for assistance with field collections, Tomoko Sakishima for assistance with greenhouse sample collection and DNA extractions, the College of Agriculture, Forestry, and Natural Resource Management at the University of Hawaii at Hilo for greenhouse space, and Angalee Kirby for greenhouse management. We are also grateful to the Genomics Core Facility at Princeton University for sequencing support and the New York University IT High Performance Computing for supplying the computational resources, services, and staff expertise. We thank Jean-Yves Meyer, Yohan Pillon, and the M.D.P. laboratory members, especially Jonathan Flowers, for valuable discussion of the manuscript. This research was funded by NSF Plant Genome Research Program (IOS-1546218), the Zegar Family Foundation (A16-0051), and the New York University Abu Dhabi Research Institute (G1205) to M.D.P., and the University of Nevada, Las Vegas College of Sciences, NSF Faculty Early Career Development Program (DEB0954274) (Principal Investigator) and Centers of Research Excellence in Science and Technology Program (HRD-0833211) (co-PI) to E.A.S.

Author contributions: J.Y.C., X.D., O.A., J.Z.P., P.R., S.H., E.H., S.J., J.F.A., M.D.P., and E.A.S. designed research; J.Y.C., X.D., O.A., J.Z.P., P.R., S.H., E.H., S.J., J.F.A., M.D.P., and E.A.S. performed research; J.Y.C. and E.A.S. analyzed data; and J.Y.C. and E.A.S. wrote the paper.

Competing interest statement: X.D., P.R., S.H., E.H., and S.J. are employees of Oxford Nanopore Technologies and are shareholders and/or share option holders.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2023801118/-/DCSupplemental.

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands - pnas.org

Cancer is the leading cause of death globally, with nearly 10 million deaths per year. Rare diseases impact more than 400 million people worldwide, and 95 percent dont have an approved treatment. In the vast majority of cases, both cancer and rare disease are diseases of the genome, caused by mono or polygenic variations. Organizations around the world are turning to genetics as the key to diagnosing and treating patients.

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Genomics England Develops Genomic and Health Information Platform on AWS - HPCwire

Before humans made their way to New Zealand, the critically endangered flightless parrot known as thekkplikely numbered in the hundreds of thousands. By 1995, their numbers had dwindled to just 51 birds, including 50 isolated on tiny Stewart Island and a single male, known as Richard Henry, all alone on the mainland. Today, those numbers have grown to about 200 individuals.

Now, the first genome sequencing of the species offers some surprisingly good news: despite 10,000 years of island isolation and inbreeding, thekkpappear to have lost potentially deleterious mutations rather than accumulating them. In fact, they now carry fewer deleterious mutations than now-extinct populations on the mainland once did. The analyses, conducted by researchers from Sweden and New Zealand, are reported today in the journalCell Genomics.

Even though thekkpis one of the most inbred and endangered bird species in the world, it has many fewer harmful mutations than expected, says Dr Nicolas Dussex, a researcher at the Center for Palaeogenetics and Stockholm University.

Our data shows that the surviving population on Stewart Island has been isolated for approximately 10,000 years and that during this time, harmful mutations have been removed by natural selection in a process called purging and that inbreeding may have facilitated it.

In small populations, this type of harmful mutation can lead to genetic diseases, adds ProfessorLove Daln, of the Center for Palaeogenetics and Swedish Museum of Natural History.

Our finding of a reduced number of harmful mutations is therefore important, since it means that inbreeding in the present-day population is likely to have less severe impact than we had initially thought.

In the new study, the researchers report the first genome-wide analyses of thekkp, including a high-quality genome assembly. All together, they sequenced and analyzed 49kkpgenomes, including 35 representing members of the sole surviving island population and 14 representatives from the extinct mainland population.

In small populations, scientific theory suggests that deleterious mutations may accumulate, leading to an increased risk for extinction. But its also possible that detrimental gene variants, exposed through inbreeding, could instead be eliminated from the population by natural selection, a process known as purging. In the new study, the researchers now find that the latter possibility more accurately describes whats happened in the case of thekkp.

The researchers say that the findings can now be put to practical use in efforts to protect and grow the remaining population. For example, the genome data can be used to select breeding individuals that may be most helpful for future generations.

We show that the single male survivor from the mainland, Richard Henry, has more harmful mutations than Stewart Island birds, ProfessorDalnsays.

Therefore, there could be a risk that these harmful mutations spread in future generations.

On the other hand, Richard Henry is also genetically distinct and may carry useful genetic diversity, he adds. This means that careful consideration must be given to pros and cons. It will therefore be important to carefully monitor the health and genomes of Richard Henrys offspring to ensure they dont introduce harmful mutations to the island population.

The findings inkkpalso have implications for endangered and small populations more broadly.

Our results are good news, not only forkkpbut also for the conservation of other highly inbred and isolated species, because they suggest that it is possible, under some circumstances, for small populations to survive even if isolated for hundreds of generations, says Professor Bruce Robertson, of the University of OtagosDepartment of Zoology, who has studiedkkpgenetics for 25 years.

While the species is still critically endangered, this result is encouraging as it shows that a large number of genetic defects have been lost over time and that high inbreeding alone may not necessarily mean that the species is doomed to extinction, Dr Dussex says.

It thus gives us some hope for the long-term survival of thekkpas well as other species with a similar population history.

The researchers plan to continue investigating other extremely inbred avian and mammalian species to produce studies similar to this one. An important goal is to find out whether the health of todayskkpis a rare exception, whereas most endangered species instead tend to accumulate harmful mutations.

Reference: Dussex N, van der Valk T, Morales HE, et al. Population genomics of the critically endangered kkp. Cell Genomics. doi: 10.1016/j.xgen.2021.100002.This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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Despite Years of Inbreeding, Kkp Are in Good Genetic Health - Technology Networks