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Plants adaptations to and divergence in arid deserts have long fascinated scientists and the general public. Here, we present a genomic analysis of two congeneric desert plant species that clarifies their evolutionary history and shows that their common ancestor arose from a hybrid polyploidization, which provided genomic foundations for their survival in deserts. The whole-genome duplication was followed by translocation-based rearrangements of the ancestral chromosomes. Rapid evolution of genes in these reshuffled chromosomes contributed greatly to the divergences of the two species in desert microhabitats during which gene flow was continuous. Our results provide insights into plant adaptation in the arid deserts and highlight the significance of polyploidy-driven chromosomal structural variations in species divergence.

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

As individuals of each plant species cannot simply move to avoid stresses, biologists since Darwins era have been fascinated by their adaptations to environments with harsh climatic conditions such as deserts (1, 2). Several mechanisms generate novel genetic variation that enables plants to adapt to their environment, such as point mutation, gene duplication, and polyploidization (35). As one of these mechanisms, whole-genome duplication (WGD) or polyploidization, has frequently occurred throughout the evolutionary history of plants (68), and many polyploidization events have putative associations with environmental changes and subsequent adaptation to new niches (9, 10). Two types of polyploidy are recognized in plants and other organisms: autopolyploidy (involving duplication of a single species genome) and allopolyploidy (involving combination of different species genomes) (7, 11). The relative proportion of autopolyploids and allopolyploids are comparable, but allopolyploidy is generally expected to provide higher adaptive potential (12, 13). This is because it not only allows the pairing of chromosomes from each parent, with diploid-like meiotic behavior and disomic inheritance, but also leads to extensive chromosomal structural variations, morphological innovations, novel genic interactions, and hybrid vigor (7, 14). Such evolutionary consequences have been repeatedly confirmed in allopolyploid model species, for example, Arabidopsis, and widely cultivated allopolyploid crops, including cotton, wheat, and oilseed rape (1519).

In general, polyploid plants exhibit higher drought and salt tolerance than their diploid relatives (1215); however, little is known about how subsequent speciation and diversification occur in such polyploid genomes. To improve such understanding, we examined the contribution of polyploidization (if any) to adaptive evolution and speciation in the bispecific genus Pugionium, endemic to the Kubuqi Desert and Mu Us Desert in northwestern China (20). These inland deserts arose from rapid climate transformation since the early Miocene (21, 22), with consequent changes in vegetation, forest retreats, and the emergence of aridity-adapted species (23). The genus Pugionium belongs to the family Brassicaceae, which includes more than 3,700 species distributed around the world (24, 25). Many species of Brassicaceae are economically important crops that are cultivated as vegetables, condiments, fodder, and oilseeds (18, 24, 26). In addition, allopolyploidyusually associated with chromosomal structural variations (fusion, shuffling, or translocation) and changes in chromosome base numberis prevalent in the family (24, 2729). Brassicaceae are divided into five major lineages (24), and Pugionium belongs to Expanded Lineage II with isolated position (30). Although young leaves and shoots of Pugionium are consumed as vegetables by local communities (23), both species produce highly lignified roots, stems, and silicles, which have a clear adaptive value in dry and salty deserts. Pugionium cornutum has long roots and an erect stem that can be more than 1.5 m tall, while Pugionium dolabratum produces short roots and numerous basal bushy branches (Fig. 1A). Most populations of the two species have no overlapped distributions, but they do occur rarely in the same site with distinct microhabitat divergence (23) (SI Appendix, Results). Furthermore, P. cornutum and P. dolabratum are confined to the mobile and fixed dunes, respectively (23), and also display differences in leaf and silicle morphology, including the sizes of silicle valves and wings (31). In this study, we first sequenced and assembled genomes of the two Pugionium species and then assessed the genomic changes that had taken place during the ancestral adaptation of the genus to the desert environment. Next, we examined the genomic divergence of both species at the population level to investigate how speciation might occur in the desert.

The contrasted habit and morphology of the two Pugionium species and genomic structure of P. cornutum. (A) Morphological and habitat divergence of the two species (1, 2, and 3 for P. cornutum and 4, 5, and 6 for P. dolabratum) on the basal branching and stem height, leaf (lobe width), silique morphology (valve and wing length and angle ), and habitat (mobile and fixed dunes). (Scale bar: 1 cm.) (B) Collinearity within the P. cornutum genome. Color-coded lines in the middle (1) show gene synteny between chromosomes. Histograms from inside to outside show frequencies of tandem repeats (2), LTR/Gypsy retrotransposons (3), LTR/Copia retrotransposons (4), overall repetitive contents (5), and densities of genes (6), respectively.

Our examination of DAPI-stained mitotic chromosome spreads revealed 11 chromosome pairs (2n = 22) in both Pugionium species (SI Appendix, Fig. S1). The genome sizes were estimated to be 570 and 606 Mb for P. cornutum and P. dolabratum, respectively (SI Appendix, Figs. S2 and S3). A high-quality reference genome of P. cornutum was obtained with 81.3 Gb (143x) Nanopore long reads and 44.7 Gb (78x) short reads (SI Appendix, Table S1). With the aid of the chromosome conformation capture technique (SI Appendix, Fig. S4), the genome of P. cornutum was further assembled into 11 chromosomes (Fig. 1B and SI Appendix, Fig. S5). The resulting assembly of P. cornutum was 550 Mb, with a scaffold N50 of 37.1 Mb and a contig N50 of 311.7 kb (SI Appendix, Table S2). For P. dolabratum, 211 Gb (356x) short reads and 10.7 Gb (18x) Pacbio long reads were used to de novo assemble the genome into large scaffolds, with scaffold N50 being 357.8 kb and contig N50 being 68.4 kb (SI Appendix, Tables S3 and S4). We assessed the quality of genome assemblies using RNA sequencing (RNA-seq ) data obtained from roots, stems, leaves, and flowers (SI Appendix, Table S5). The results showed that most coding regions were well represented in the assemblies (SI Appendix, Table S6). Moreover, 97.9 and 97.4% of the 2,326 eudicot-specific BUSCO genes were identified in the genome assemblies of P. cornutum and P. dolabratum, respectively (SI Appendix, Table S7).

In total, 72.8 and 65.0% of the genome sequences were identified as repetitive elements for P. cornutum and P. dolabratum, respectively (Fig. 1B and SI Appendix, Tables S8 and S9), and the vast majority of repeats were classified as tandem repeats and long terminal repeat (LTR ) retrotransposons. An analysis of LTR retrotransposons indicated an increase in the activity during the last three million years (SI Appendix, Fig. S6). A total of 31,412 and 30,614 protein-coding genes were predicted for P. cornutum and P. dolabratum, respectively (SI Appendix, Table S10), and 27,982 (89.1%) of these genes were distributed on the assembled chromosomes of P. cornutum. In addition, most of these genes were successfully annotated by at least one public database (SI Appendix, Table S11), with complete BUSCO scores of 95.1 and 94.2% for P. cornutum and P. dolabratum, respectively (SI Appendix, Table S12), indicating near completion of both the assemblies and annotations.

Our comparative chromosome painting analyses based on cross-species hybridization, using BAC contigs specific to the chromosomes of Arabidopsis thaliana, suggested two copies of genomic blocks (GBs) in the Pugionium pachytene chromosome complements (SI Appendix, Fig. S7). This pointed to a potential WGD (tetraploidization) that had occurred during the origin of Pugionium. This WGD was further confirmed by genome collinearity and synonymous divergences of paralogous gene pairs within collinear blocks (Fig. 1B and SI Appendix, Figs. S8S11). Based on the divergence of paralogous gene pairs, this WGD was estimated to have occurred 18 Mya (SI Appendix, Fig. S9) when Lineages I and II diverged (30, 32) and was more recent than the family-specific At- WGD (43 Mya) (33). Phylogenetic analyses of different datasets were then performed to examine whether the tetraploidy arose from autopolyploidization or allopolyploidization. We first constructed gene trees using six species, that is, P. cornutum, Arabidopsis lyrata, Capsella rubella, Eutrema salsugineum, Schrenkiella parvula, and Aethionema arabicum, and assessed the pattern of gene tree topologies. For the 5,461 genes that were single copy in each of the six genomes, the placement of P. cornutum as sister to Lineage II was supported by 42.0% (bootstrap supports 70% ) of gene trees, while 17.8% (bootstrap supports 70%) placed P. cornutum sister to Lineage I plus II (SI Appendix, Fig. S12), suggesting a likely hybrid origin because of the high inconsistent tree topologies. Then, we carried out phylogenetic analyses of the two duplicate paralogs from the At- polyploidization and the possible homologs in Pugionium and Eutrema. Most duplicated homologs in Pugionium did not cluster into one monophyletic group as expected for autopolyploidization (SI Appendix, Fig. S12). Finally, 8,268 gene trees constructed based on homolog groups that contain one gene from A. arabicum and at least one homolog in all other genomes were used to perform multilabeled trees (MUL-trees) analysis, and the optimal MUL-tree also supported an allopolyploid origin of P. cornutum (SI Appendix, Fig. S13).

In order to further confirm allopolyploidization and uncover the origin of the two parental Pugionium (sub)genomes, the genome of P. cornutum was used to examine the association of GBs specific to previously defined ancestral Brassicaceae genomesancestral Proto-Calepineae Karyotype (ancPCK, n = 8) (29) and Proto-Calepineae Karyotype (PCK, n = 7) (27). The conserved association of blocks K-L and M-N on Pugionium chromosome 3 indicated that one parental (sub)genome was ancPCK-like (denoted as SG1, Fig. 2A and SI Appendix, Fig. S14). In contrast, the association K-L+Wa on Pugionium chromosome 9 pointed to a PCK-like (sub)genome (denoted as SG2). Despite the extensive postpolyploidization shuffling, these comparative analyses have collectively shown that the ancestral Pugionium genome originated through an allotetraploid WGD based on hybridization between ancPCK- and PCK-like genomes (Fig. 2A). This ancestral allopolyploid genome experienced an extensive postpolyploid diploidization, reducing the chromosome number from n = 15 to n = 11 (Fig. 2A). Among the 11 chromosomes in the Pugionium genome, five chromosomes remained conserved (chromosomes 1, 2, 6, 10 and 11), whereas the remaining six chromosomes were greatly reshuffled by translocations and inversions (Fig. 2A). Three chromosomes (3, 4, 7) showed high chromosomal structural variations as compared to the ancestral genomes.

The origin and postpolyploid evolution of the allotetraploid Pugionium genome. (A) The ancestral Pugionium genome presumably originated from hybridization between an ancPCK-like genome (n = 8, subgenome SG1) and a PCK-like genome (n = 7, subgenome SG2). Capital letters denote GBs and their associations important for inferring the ancestral (sub)genomes. (B) Phylogenetic tree for Pugionium and 11 other plants. A WGD was identified in Pugionium, paralleling independent mesohexaploidy events in Leavenworthia and Brassica. More changes in the numbers of gene family members apparently occurred in the ancestor of P. cornutum and P. dolabratum because of polyploidization than in the ancestor of E. salsugineum and Brassica rapa. (C) The seven phenylalanine ammonia-lyase (PAL) genes on three Pugionium chromosomes derived from allopolyploidization. (D) Collinear gene blocks between Pugionium and E. salsugineum indicate that genes of the PAL family from both ancestral parents were retained in Pugionium; other collinear genes are shown in yellow, and genes not in collinear blocks are displayed in creamy white.

According to their associated gene tree topologies, duplicated GBs in the genome of P. cornutum were partitioned into subgenomes SG1 and SG2 (SI Appendix, Figs. S15 and S16 and Table S13). Based on the modeled postpolyploidization interchromosomal rearrangements and loss of chromosomal segments (SI Appendix, Fig. S14), we identified a total of 10,985 and 14,936 protein-coding genes in the subgenome SG1 and SG2, respectively. Here, biased fractionation resulted in the preferential retention of genes from one parental genome (SI Appendix, Table S14). Based on these 14,936 genes, which were phylogenetically closer to Lineage II, the divergence time between subgenome SG2 and E. salsugineum was estimated to be 12 Mya. This suggests that the allotetraploid WGD recovered for Pugionium or with its related but unsampled genera should have occurred around this age or later. We then examined expression levels of the homeologous gene pairs in order to investigate the presence or absence of the subgenome dominance. Using RNA-seq data from different tissues, we found biased gene expressions between the two subgenomes with genes located in the subgenome SG2 having significantly higher expression than those from SG1 (SI Appendix, Figs. S17 and S18). In addition, around 42.0% of the homoeologous gene pairs were estimated to show at least twofold differentiated expressions between the two subgenomes (SI Appendix, Fig. S19).

We next determined gene families experienced expansion and contraction in the Pugionium genus based on annotated genomes of the two Pugionium species and other species from Brassicaceae (Fig. 2B and SI Appendix, Table S15). Out of the 2,466 gene families specifically expanded in Pugionium, 2,143 contained duplicated genes derived from WGD as determined by the presence of collinear blocks. Gene families expanded via WGD were enriched in multiple Gene Ontology categories related to organ developments and stress responses, including leaf development, root development, seed development, cellular response to salt stress, and response to light stimulus, while those expanded via tandem duplications were overrepresented in functional categories associated with root meristem growth, secondary metabolite biosynthetic process, and DNA (cytosine-5-)-methyltransferase activity (Datasets S1 and S2). We found that 40 out of 58 transcription factor gene families had expanded in Pugionium (SI Appendix, Table S16). Most of them are involved in responses to abiotic stress. For example, members of RAV and GRAS gene families were reported to respond to salty and cold stresses. In addition, we found that gene families related to ionic and osmotic equilibrium (CIPK and CDPK), drought tolerance (ABF and DREBs), and lignin biosynthetic pathway (PAL and MSBP) were also expanded within Pugionium (Fig. 2 C and D and SI Appendix, Figs. S20S22 and Tables S17S19). Expansions of these gene families should have supplied genetic foundations for this genus to adapt to the challenging habitats. In addition, we also found that genes located in the subgenome SG2 showed higher expression levels than those in SG1 in these gene families, which further confirmed that the biased gene expression played a likely role for plant adaptation during diploidization after allopolyploidization (SI Appendix, Table S18).

In addition to morphological differentiation (Fig. 1A), two Pugionium species appear to show local adaptation to different microhabitats (SI Appendix, Figs. S23S26 and Tables S20S23) as found for other closely related desert plants (34). To explore the genetic basis of the divergence, we conducted whole-genome resequencing of five populations (a total of 20 individuals) for each species (Fig. 3A and SI Appendix, Table S24). The linkage disequilibrium of both species decayed to half maximum within 5 kb (Fig. 3B). The principal component (PC) analysis distinguished the two species along PC1 (variance explained 19.1%, TracyWidom P = 3.0 1013; Fig. 3C), and our population structure analysis similarly revealed two distinct genetic clusters (Fig. 3D and SI Appendix, Fig. S27). We then evaluated four models of speciation, that is, strict isolation, isolation with migration, isolation after migration, and secondary contact (SI Appendix, Fig. S28 and Table S25), using a composite likelihood approach. The best-fit model suggested that two Pugionium species diverged with a continuous gene flow (SI Appendix, Table S26) around 1.65 Mya (Fig. 3E), suggesting sympatric or parapatric speciation through microhabitat selections.

Population structure and interspecies divergence of Pugionium. (A) Locations of 10 sampled populations. (B) Linkage disequilibrium decay based on the squared correlation coefficient between SNPs in P. cornutum and P. dolabratum populations. (C) Results of the PC analyses of SNPs within the two species. (D) Population structure of all sampled individuals of the two species (with K = 2 as the best inferred value). (E) The best-fit demographic divergence of the two species modeled by fastsimcoal2. Effective population sizes, divergence time and estimates of gene flow between species are displayed on the schematic plot. MYA, million years ago. (F) Manhattan plots of FST, dXY, , and between and within the two Pugionium species using a 50-kb nonoverlapping window. Genomic regions of high divergence in 11 chromosomes (Top) and genes under selection in those regions on chromosome 4 and 7 (Bottom) are highlighted in red. Pco, P. cornutum; Pdo, P. dolabratum.

We identified a total of 42 genomic regions (50 kb in size) in assembled chromosomes of P. cornutum that exhibited high divergence between P. cornutum and P. dolabratum (i.e., upper 1% of the empirical FST distribution) (SI Appendix, Table S27), which also had significantly elevated dXY compared to other genomic regions (P = 2.1 1013, MannWhitney U test; Fig. 3F). Out of these 42 regions, 27 and 15 were identified in subgenome SG1 and SG2, respectively, without biased distributions (P = 0.06) (Fig. 3F and SI Appendix, Table S27). However, 86% of these regions were found to be located on chromosomes 3, 4, and 7 (Fig. 3F), which were formed by recombination among multiple ancestral chromosomes (SI Appendix, Fig. S14). Genome-wide FST and dXY were positively correlated, especially for the three chromosomes (SI Appendix, Fig. S29). Furthermore, nucleotide diversity was found to be significantly lower in these regions for both P. cornutum (P = 5.3 1015) and P. dolabratum (P < 2.2 1016; Fig. 3F), suggesting that selection might have acted on these regions. A total of 236 genes were identified from these highly divergent regions, and the vast majority of these genes were found to be located on chromosome 4 (68.6%) and 7 (28.8%). The expression of some of these genes in four different tissues showed contrasting difference between the two species (SI Appendix, Figs. S30 and S31). Using a HudsonKreitmanAguad test, 197 of these genes were inferred to be under selection, and most of them were located in subgenome SG2 (SI Appendix, Table S28). Homologs of these genes were identified to be involved in root development (BDG1, KUA1, ABCB4, GH3.9), leaf morphogenesis (AS2, KUA1, FL6, GRF3), xylem differentiation (LHL3), seed germination and seedling development (NAC25, MED7B, STM), salt tolerance (BHLH112, GolS1, TSPO), drought resistance (BDG1, PUB23), oxidative stress response (NUDT2), and flavonoid biosynthesis (MYB12) (Fig. 3F). The two Pugionium species have distinct differences in morphology and habitat, with P. cornutum only occurring on mobile dunes, whereas P. dolabratum is distributed in fixed or semifixed deserts (Fig. 1A). They displayed contrasting patterns in seed germination speed and growth rate in response to salinity stress and desert burials (SI Appendix, Figs. S23S26 and Table S23). Therefore, the divergence selection of those genes might be responsible for morphological differentiation of root, shoot, and leaf and further contributed to local adaptation of the two Pugionium species to different microhabitats.

To further test whether copy number variations of specific gene families between the two species contributed to speciation, we used the two de novo genomes to identify the genes of three amino acid loop extension (TALE) and histidine kinases (HKs) gene families, members of which were revealed to have crucial functions in regulating various development processes and responses to abiotic stress in plants (SI Appendix). Compared to other Brassicaceae species, these families were expanded in both Pugionium species but with interspecific copy number variations between them (SI Appendix, Figs. S32 and S33 and Table S29). In the TALE gene family, we found that P. dolabratum contained more copies for BLH11, KNAT2, and KNAT6 compared with P. cornutum. The BLH11 ortholog from Medicago truncatula (PINNA1) was identified as a determinacy factor during leaf morphogenesis (35). In Arabidopsis, KNAT2 and KNAT6 were also confirmed to play essential roles in regulating proximaldistal development of leaves by the repression from AS2 (36), which was also found to have experienced positive selection in the two Pugionium species (SI Appendix, Table S28). For the HKs gene family, more homologic copies were detected in P. cornutum for AHK2 and AHK4, which encode two cytokinin receptors involved in shoot and root development, as well as tolerance to salt and drought stress (3739). In addition, expression divergence of these gene copies was also detected between the two species (SI Appendix, Figs. S32 and S33). Thus, the copy number variations in these gene families may also have contributed to the morphological divergences between the two species as well as the respective adaptations to mobile and stable desert dunes.

Based on comparative chromosome painting analyses (SI Appendix, Fig. S7) and divergence distributions of the paired paralogs, we inferred the occurrence of a WGD presumably specific to the genus Pugionium and clear postpolyploid chromosomal structural variation. Further analyses suggested that this WGD probably involved allopolyploidization rather than autopolyploidization and occurred around 12 Mya or later, postdating the divergence of two ancestral parental lineages (n = 8 and 7, respectively; Fig. 2A) 18 Mya. Similar allopolyploidizations, involving ancPCK- and PCK-like parental genomes, were previously reported in the genus Ricotia (n = 13 and 14) (40) and Lunaria (n = 14) (41). However, the ancestral allopolyploid Pugionium genome experienced more extensive descending dysploidy (from n = 15 to n = 11) during its postpolyploid diploidization, associated with the origin of three highly rearranged chromosomes (Fig. 2A). The allopolyploid origin of Pugionium seems to have facilitated its survival through adaptation to the changing environments of northwest China during their desertification since the early Miocene (21, 42). Inter alia, gene families involved in drought tolerance, ionic and osmotic equilibrium, and lignin biosynthesis expanded in the Pugionium genomes significantly (SI Appendix, Fig. S20 and Table S17).

Genomic evidence indicates that the two species started to diverge around 1.65 Mya, during the Quaternary, when a global increase in aridity (20, 43, 44) might have led to the development of contrasting desert microhabitats, mobile and fixed dunes, thereby promoting the initial divergence of the two species through microhabitat adaptation with parapatric or sympatric distribution. This hypothesis is corroborated by our speciation modeling of joint site frequency spectra across the total genome, which suggests the occurrence of continuous and strong gene flow through their evolutionary divergence history. We further found that the high-divergence regions in the Pugionium allopolyploid genome were mainly distributed on three chromosomes with most structural variations generated by translocation-based reshuffling during postpolyploidization diploidization. In addition to copy number variations of gene families, genes with positive selection signals in these regions are highly involved in root development, leaf morphogenesis, and microhabitat adaptation (seed germination and dry/salt tolerance), corresponding well with interspecific divergences in these respects (SI Appendix, Tables S21 and S23). Therefore, our results suggest that polyploidy-driven chromosomal structural variation may have played an important role in subsequent speciation and further extensive diversification (45) in addition to well-known rapid differentiations of the duplicated genes and novel genic interactions (46).

Mitotic chromosome spreads were used primarily for chromosome counting and pachytene spreads for comparative chromosome painting analysis. Long reads were generated using GridION and PacBio RS II. Paired-end and mate-pair short reads were generated using the MGISeq 2000 and Illumina HiSeq platforms. Genomes were assembled using MaSuRCA. Transposable elements were identified using Tandem Repeats Finder, RepeatMasker, RepeatModeler, and LTR_Finder. Genes were predicted using AUGUSTUS, GlimmerHMM, PASA, Exonerate, and EVidenceModeler. Collinear gene blocks were identified with MCscanX. Synonymous substitution rates were calculated using PAML. Following genome alignments and chaining by LASTZ, GRAMPA was used to determine the likeliest mode of polyploidy. Gene expression levels were estimated using Salmon and DESeq. Clean reads from population data were mapped to the P. cornutum genome using the bwa-men algorithm. Genome-wide single nucleotide polymorphisms (SNPs) were called by GATK. ADMIXTURE and Eigensoft were used for population structure analysis. Coalescence-based simulation of speciation patterns was performed in fastsimcoal2. The interspecific reproductive isolation within the genus, and differences between the two species in microhabitat adaptation, were experimentally confirmed at desert sites. Detailed information on all the experimental and analytical procedures is available in SI Appendix.

The whole-genome sequencing data, transcriptome sequencing data, and genome assemblies have been deposited in the National Center for Biotechnology Information Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) under accession numbers PRJNA685118 and PRJNA760666.

This work was equally supported by the Second Tibetan Plateau Scientific Expedition and Research program (2019QZKK0502), the National Natural Science Foundation of China (91731301, 91331102, and 41771055), and also the Fundamental Research Funds for the Central Universities (SCU2021D006 and 2020SCUNL207). T.M. and M.A.L. were supported by the Central European Institute of Technology 2020 project (LQ1601).

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

Reviewers: M.A.B., The University of Arizona; and L.L., Fudan University.

The authors declare no competing interest.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2025711118/-/DCSupplemental.

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Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation - pnas.org

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Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway - Nature.com

SAN DIEGO, Oct. 15, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO), developer of the Saphyr system that uses optical genome mapping (OGM) for the detection and analysis of structural variants (SVs), today announced the American Society of Human Genetics (ASHG) conference lineup of customer posters and presentations featuring OGM. The customer posters and presentations span genetic disease applications including amyotrophic lateral sclerosis (ALS) and postnatal, as well as cancer research applications including pediatric brain tumors and myelodysplastic syndromes (MDS). The ASHG conference is being held virtually this year and runs from Monday, October 18, 2021 to Friday, October 22, 2021.

Talks featuring Bionano Genomics OGM solutions include research into how structural variation contributes to the cause of ALS; inverted genomic triplication structures; and a multi-site clinical validation study of constitutional postnatal SV, CNV and repeat array sizing, as well as findings of SVs in pediatric brain tumors, and epigenetics. Below is a list of customer presentations featuring OGM at this years ASHG conference.

OGM Application Area

Presenter

Affiliation

Presentation Title

Inherited Genetic Disorders

Dr. C.M. Grochowski

Baylor College of Medicine

Inverted genomic triplication structures: two breakpoint junctions, several possibilities

Dr. Emily McCann

Macquarie Univ. Ctr. for MND Research, Sydney, Australia

Development of a discovery pipeline for structural variation contributing to the cause of amyotrophic lateral sclerosis

Dr. Nikhil Sahajpal

Agusta University, Praxisgenomics, University of Iowa Hospital

Optical Genome Mapping for Constitutional Postnatal SV, CNV, and Repeat Array Sizing: A Multisite Clinical Validation Study

Dr. Ravindra Kolhe

Augusta University

Large-Scale, Multi-site, Postnatal Studies on Optical Genome Mapping (OGM)

Hematological Malignancies

Dr. Rashmi Kanagal-Shamanna

MD Anderson Cancer Center

Optical Genome Mapping Improves the Clinically Relevant Structural Variant Detection in MDS

Dr. Gordana Raca

Children's Hospital Los Angeles

Utilization of Optical Genome Mapping in Detection and Characterization of Rare Genetic Markers in Pediatric Leukemias

Solid Tumor Analysis

Dr. Miriam Bornhorst

Childrens National Hospital

Optical genome mapping reveals novel structural variants in pediatric brain tumors

Epigenetics Application

Dr. Surajit Bhattacharya

Childrens National Hospital

Utilization of Dual-Label Optical Genome Mapping for genetic/epigenetic diagnosis

We are delighted to see the broad range of presentations on OGM at ASHG this year, stated Erik Holmlin, PhD, CEO of Bionano Genomics. Our customers continue to push forward conducting cutting-edge research in the human genetics space and we are excited for them to share their research with the ASHG community. Congratulations to the authors on their work and the recognition that comes with delivering presentations at this important conference.

Story continues

For more details and to register for this online event please go to: https://www.ashg.org/meetings/2021meeting/

About Bionano Genomics

Bionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing; it also provides diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a research use only platform for ultra-sensitive and ultra-specific structural variation detection that enables scientists and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools. Bionano offers genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for more than nine years and has performed more than 65,000 tests for those with neurodevelopmental concerns. For more information, visit bionanogenomics.com or lineagen.com.

Forward-Looking Statements of Bionano Genomics

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the timing and content of the posters and presentations regarding OGM to be presented at the ASHG conference. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the accuracy of customer posters and presentations to be presented; observations from studies covered by the posters and presentations may not be replicated; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2020 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on managements assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

Media Relations:Michael SullivanSeismic+1 (503) 799-7520michael@teamseismic.com

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Bionano Genomics Announces American Society of Human Genetics Presentations Featuring Optical Genome Mapping for Genetic Disease and Cancer Research...

The Covid-19 crisis that gripped the UK between September 2020 and June 2021 can be thought of as a series of overlapping epidemics, rather than a single event, say researchers at the Wellcome Sanger Institute, EMBLs European Bioinformatics Institute (EMBL-EBI) and their collaborators. During this period, the country wrestled with several versions of the SARS-CoV-2 virus that possessed different biological properties and required a different public health response.

The study, published today (14 October) in Nature, is the most detailed analysis of SARS-CoV-2 genomic surveillance information to date. It describes the scientific story of the pandemic as it unfolded and underlines the importance of high-speed, large-scale genomic surveillance to understand and respond to infectious outbreaks.

In March 2020, just as the UK was preparing to enter the first of several lockdowns, the Covid-19 Genomics UK (COG-UK) consortium was set up to monitor the spread and evolution of SARS-CoV-2 by sequencing the viruss genome1.

Since then, the consortium has identified and monitored numerous viral variants, including the Alpha variant first identified in Kent in September 2020 and the Delta variant first identified in India in April 2021. Both of these variants subsequently changed the course of the pandemic, not only in the UK but globally.

For this study, researchers at the Wellcome Sanger Institute and EMBL-EBI analysed SARS-CoV-2 genomic surveillance data from England2 collected between September 2020 and June 2021. They characterised the growth rates and geographic spread of 71 lineages and reconstructed how newly emerging variants changed the course of the epidemic.

At the end of 2020, the Alpha variant (B.1.1.7) spread despite a series of restrictions, including a national lockdown in November and regional restrictions in December. Though these measures slowed the spread of other variants, Alpha was found to possess a 50 to 60 per cent growth advantage over previous variants and continued to spread rapidly.

In the system of tiered restrictions operating in December 2020, infection rates were higher in areas with fewer restrictions. Alpha was only brought under control in a third national lockdown between January and March 2021, which was introduced after a peak of 72,088 daily cases on 29 December. This measure simultaneously eliminated most variants that had been dominant in September and October 2020. When restrictions began to be lifted on 8 March 2021, the daily case rate had fallen to 5,500.

While Alpha was being brought under control, variants associated with a greater ability to circumvent immunity from vaccination or prior infection continued to appear in the UK at low levels in early 2021. These variants were characterised by the spike mutation E484K, the most significant of which were the Beta variant (B.1.351, first identified in South Africa) and Gamma variant (P.1, first identified in Brazil). But despite repeated introductions of these variants, they were confined to short-lived local outbreaks.

In March 2021, the first samples of B.1.617, which originated in India, began appearing in sequence data. This was in fact two lineages, Kappa (B.1.617.1) and Delta (B.1.617.2). Though Delta contained different mutations to previous variants of concern, these mutations achieved even greater transmissibility3. While Kappa grew slowly and has since faded away, Delta had spread to all local authorities and accounted for 98 per cent of viral genomes sequenced by 26 June 2021.

Dr Moritz Gerstung, a senior author of the paper from EMBL-EBI and The German Cancer Research Centre (Deutsches Krebsforschungszentrum, DKFZ), said: Time has proven how ingenious an idea it was to set up the Covid-19 Genomics UK (COG-UK) consortium at the beginning of the pandemic. Being able to see lineages side-by-side, mapped to specific locations, has been incredibly informative in terms of understanding how this series of epidemics has unfolded. To see Alpha growing faster in nearly 250 out of 315 local authorities was a clear signal that we were dealing with something very different. At the same time, weve learned that the genetics of SARS-CoV-2 are incredibly complex. Even though we knew all of Deltas mutations, it wasnt immediately clear that it would become the dominant lineage, for example.

Analysis of Delta indicates that its growth rate was 59 per cent higher than that of Alpha, the greatest growth advantage observed in any other variant to date. Overall, the researchers estimate that the spread of more transmissible variants between August 2020 and the early summer of 2021 more than doubled the average growth rate of the virus in England.

Dr Meera Chand, COVID-19 incident director at the UK Health Security Agency (UKHSA) and one of the authors of the paper, said: Thanks to genomic surveillance in the UK and internationally, it is clear that we are dealing a virus that has changed considerably since the one that we faced in March 2020. We will continue to monitor the SARS-CoV-2 virus to ensure that we can use the most effective vaccines, treatments and public health measures against current and future variants.

Although it remains impossible to predict what the virus will do next, the COG-UK consortium has advanced the field of genomic surveillance considerably and proven the value of monitoring for infectious agents. Just 18 months after its inception, the programme catalysed the establishment of national sequencing systems that provide near real-time epidemiological information to inform the UKs public health response. It is hoped that one day scientists will be able to predict the emergence of new variants.

Dr Jeff Barrett, a senior author of the paper and Director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute, said: These genomic surveillance data have given us a totally new way of watching an outbreak unfold, which has taught us a lot about how a new infectious agent spreads and evolves. My hope is that similar genomic surveillance programmes will be developed across the world, so that we are as well-prepared as we can be to respond to future infectious disease outbreaks whether they be familiar pathogens or new ones.

ENDS

Contact details: Dr Matthew MidgleyPress OfficeWellcome Sanger InstituteCambridge, CB10 1SAPhone: 01223 494856Email: press.office@sanger.ac.uk

Notes to Editors:

1 An overview of how Covid-19 genomes are sequenced is available on the Sanger Institute blog. More information on COG-UK is available on their website.

2. These data track SARS-CoV-2 lineages in 315 Lower Tier Local Authorities (LTLAs) in England. An LTLA is an administrative region with approximately 100,000200,000 inhabitants. In total, 281,178 viral genomes were sequenced during this period.

3 Kappa and Delta contained the L452R spike protein mutation, thought to reduce antibody recognition, and P681R, which helps the virus enter human cells in a similar manner to Alphas P681H mutation. Delta contains 5 additional spike protein mutations, the consequences of which are not fully understood yet.

Publication:

Harald S. Vhringer, Theo Sanderson and Matthew Sinnott et al. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature. DOI: 10.1038/s41586-021-04069-y

Funding:

COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute.

Selected websites:

European Bioinformatics Institute (EMBL-EBI)

The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of big data by enhancing their ability to exploit complex information to make discoveries that benefit humankind.

We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease.

We are part of EMBL and are located on the Wellcome Genome Campus, one of the worlds largest concentrations of scientific and technical expertise in genomics.

Website:www.ebi.ac.uk

The Wellcome Sanger InstituteThe Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. We are open and collaborative; our data, results, tools and technologies are shared across the globe to advance science. Our ambition is vast we take on projects that are not possible anywhere else. We use the power of genome sequencing to understand and harness the information in DNA. Funded by Wellcome, we have the freedom and support to push the boundaries of genomics. Our findings are used to improve health and to understand life on Earth. Find out more at http://www.sanger.ac.uk or follow us on Twitter, Facebook, LinkedIn and on our Blog.

About Wellcome

Wellcome supports science to solve the urgent health challenges facing everyone. We support discovery research into life, health and wellbeing, and were taking on three worldwide health challenges: mental health, global heating and infectious diseases. https://wellcome.org/

Genomic reconstruction of the SARS-CoV-2 epidemic in England

14-Oct-2021

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The inside story of England COVID pandemic described in new study - EurekAlert

Welcome to OncLive On Air! Im your host today, Caroline Seymour.

OncLive On Air is a podcast from OncLive, which provides oncology professionals with the resources and information they need to provide the best patient care. In both digital and print formats, OncLive covers every angle of oncology practice, from new technology to treatment advances to important regulatory decisions.

In todays episode, sponsored by PierianDx, we had the pleasure of speaking with Lucio N. Gordan, MD, to discuss Florida Cancer Specialists move toward the full integration of in-house genomic testing.

Streamlined processes afforded by in-house genomic testing have the potential to provide clinical, collaborative, and financial benefits, according to Gordan, president and managing physician of Florida Cancer Specialists (FCS) & Research Institute, which recently expanded their in-house next-generation sequencing (NGS) capabilities.

In our exclusive interview, Gordan, also of FCS Gainesville Cancer Center, discussed the advantages of in-house genomic testing, the transition from external to internal sequencing, and the anticipated effects of the move.

Check back on Mondays and Thursdays for exclusive interviews with leading experts in the oncology field. For more updates in oncology, be sure to visit http://www.OncLive.com and sign up for our e-newsletters.

OncLive is also on social media. On Twitter, follow us at @OncLive and @OncLiveSOSS. On Facebook, like us at OncLive and OncLive State of the Science Summit and follow our OncLive page on LinkedIn.

If you liked todays episode of OncLive On Air, please consider subscribing to our podcast on Apple Podcasts, Spotify, Google Podcasts, Amazon Music, and many of your other favorite podcast platforms,* so you get a notification every time a new episode is posted. While you are there, please take a moment to rate us!

Thanks again for listening to OncLive On Air.

*OncLive On Air is available on: Apple Podcasts, Google Podcasts, Spotify, Amazon Music, Audacy, CastBox, Deezer, iHeart, JioSaavn, Listen Notes, Player FM, Podcast Addict, Podchaser, RadioPublic, and TuneIn.

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Gordan on Growing the Infrastructure for In-House Genomic Testing - OncLive

Privacy International has warned of a potentially serious breach of privacy regulations by a firm that has been awarded 169.4 million in Government contracts

Privacy campaigners have raised concerns over a Government-approved Coronavirus testing company using customer data to market its own genomics services without affirmative consent, the Byline Intelligence Team and The Citizens can reveal.

In contracts first revealed by Byline Times in November 2020, Dante Labs has been commissioned by the Government to deliver 169.4 million worth of COVID-19 testing services.

Speaking to Byline Times, Privacy Internationals legal officer Lucie Audibert said that COVID-19 testing providers should not be exploiting the various mandatory testing requirements for their own marketing and that the contact details people provide to receive results of their tests should be used for just that not to contact you at a later date to try and sell you other services.

Without providing sufficient information and obtaining valid consent, this can be a serious breach of privacy laws, she added.

When taking the details of customers who are purchasing its tests, Dante pre-populates the tickbox consenting to marketing emails. According to guidelines from the Direct Marketing Association, under GDPR rules, a person gives consent by a statement or by a clear affirmative action. That affirmative action could include ticking a box when visiting an internet website. It goes on to say that pre-ticked boxes or inactivity should therefore not constitute consent.

The Information Commissioners Office (ICO) is also clear, telling companies: Dont use pre-ticked boxes or any other method of default consent.

A Dante customer, who was subsequently targeted by the firm with marketing emails, said that they immediately felt like my data and samples might be used for something else or for something that I might not really be aware of and that when you take a PCR COVID test with Dante Labs, they ask you many questions, including your ethnicity.

Under the UKs General Data Protection Regulation (GDPR)and PECR regulations, it is not permissible for companies to use data gathered for one purpose to then be used for another without the individuals consent. Further, companies need to obtain explicit, informed consent to market other services to customers.

Dante Labs privacy policy states that based on your consent, Dante Labs can, furthermore, process your email address to send you newsletters and marketing communications.

One email promoted Dantes Kurix Premium service, a whole genome sequencing test. It was sent to customers who had ordered a Dante PCR COVID test when travelling abroad.

A spokesperson for the Information Commissioners Office said: Businesses should only contact individuals for electronic marketing purposes where consent has been provided or, in limited circumstances, where they have an existing relationship with a customer. If anyone has concerns about how their data has been handled, they can report these concerns to us.

The Government is at the start of proposing a new data regime to replace GDPR, a law introduced by the EU. The digital rights organisation, Open Rights Group, has warned that Government plans would grant unprecedented freedom to collect, use, and share information regarding buying habits, social relationships, creditworthiness, lifestyle, hobbies, and personality of parents and children for marketing purposes.

If data protections in the UK are watered-down, stories like this could become far morefrequent.

Dante Labs and the company it owns, Immensa Health, have both won large contracts to deliver COVID-19 testing services. In this way, the firms are able to collect data from large numbers of people who are dependent on taking PCR tests to go about their daily lives, including to travel.

This access to a wide and captive customer base is behind the concerns that Dante may be exploiting mandatory testing requirements as suggested by Audibert.

In July, Dante Labs took over one of the Governments Lighthouse Labs, designed to fast-track COVID-19 testing. BusinessLive said that Dante Labs would be delivering COVID-19 testing and clinical whole genome sequencing on a large scale at the lab.

Immensa Health has won two Government contracts for PCR testing worth169,435,000. The largest of the two contracts worth 119,035,000 was awarded without competition under emergency contracting regulations. At the time, Immensa Health had only been founded four months previously.

Immensa has been named as a preferred company in a number of Department of Health and Social Care framework contracts, including as one of 50 suppliers listed in a 15 billion framework agreement for clinical laboratory diagnostic testing services. Immensa is also listed as a supplier in two smaller microbiology framework contracts worth a total of 4 billion across numerous suppliers.

Dante Labs has been expanding significantly in the UK, buying Cambridge Cancer Genomics a leader in machine learning for clinical oncology and is investing 30 million in the UK to run a global surveillance programme of the new variants of the SARS-CoV-2 virus.

A Dante Labs spokesperson told Byline Times: We do not share genetic data with any parties beyond Immensa, a Dante Labs company, and Public Health England, as per Government requirements. The sharing of relevant data with PHE is mandatory and is helping the UK to track the progression of potential COVID-19 variants which, unless monitored closely, could cost many thousands of lives. We do not sell this data, whether individual or aggregated.

Dante Labs did not respond to multiple requests for comment regarding its internal use of customer data. However, after the Byline Intelligence Team contacted the firm, it appeared to have deleted the page that was featured in its marketing emails about Kurix Premium.

Dante is also under investigation by the Competition and Markets Authority (CMA), due to concerns over its treatment of customers. There have been complaints that Dante has been not delivering PCR tests and/or results on time or at all; that it has been failing to respond to complaints or provide proper customer service; refusing or delaying refunds when requested; and using T&Cs which may unfairly limit consumers rights.

It was further revealed on 15 October that at least 43,000 people in the UK may have been wrongly given a negative COVID test by a private laboratory in Wolverhampton, run by Immensa Health Clinic. Operations have now been suspended at the lab.

This article was produced by theByline Intelligence Team a collaborative investigative project formed byByline Times with The Citizens. If you would like to find out more about the Intelligence Team and how to fund its work,click on the button below.

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Genomic Marketing of COVID Testing Company Without People's Affirmative Consent Byline Times - Byline Times

Dr Mishra | (Pic: Edexlive)

In another milestone achieved by Centurion University, Dr Rukmini Mishra, Associate Professor, Department of Botany, School of Applied Sciences, has received a grant titled Engineering Anthracnose Resistance in Chilli Pepper (Capsicum annuum L) using a Single Transcript CRISPR/Cas9 Genome Editing System under the SERB POWER Grant scheme by Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India.

The study will aim at developing a single transcript CRISPR/Cas9 gene-editing platform to introduce sequence-specific mutations at the targeted genetic loci of Capsicum annuum L to engineer broad-spectrum resistance to colletotrichum truncatum, the most aggressive anthracnose pathogen in chilli pepper. It could be used as a benchmark tool for genome engineering in other important solanaceous crops such as tomato, potato and brinjal where fungal pathogenicity is still a big problem.

Prof Supriya Pattanayak, Vice-Chancellor; Dr Anita Patra, Registrar along with the faculty members of the university congratulatedDr Mishra for her achievement. Dr Mishra is currently heading the Department of Botany under the School of Applied Sciences and is also the team lead of the Centre of Genetics and Genomics at Centurion University.

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This associate professor from Centurion University is working on research that could be used as a benchmark tool for genome engineering - EdexLive