Category Archives: Genome

The Clinical Genome Conference 2014 | Reimbursement of Clinical Sequencing Tests for Patient Care
An-Dinh Nguyen interviews John Pfeifer of Washington University School of Medicine on April 3, 2014. Dr. Pfeifer will be a keynote speaker at TCGC: The Clini...

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Animals (Pleurobrachia bachei, Euplokamis dunlapae, Dryodora glandiformis, Beroe abyssicola, Bolinopsis infundibulum and Mertensiid) were collected at Friday Harbour Laboratories (Pacific North-Western Coast of USA) and maintained in running seawater for up to 2weeks. Other species were collected at the Atlantic coast of Florida and around Woods Hole, Massachusetts (Pleurobrachia pileus, Pleurobrachia sp., Mnemiopsis leidyi) as well as central Pacific (Palau, Hawaii, Coeloplana astericola, Vallicula multiformis). Animals were anaesthetized in 60% (volume/body weight) isotonic MgCl2 (337mM). Specific tissues were surgically removed with sterile fine forceps and scissors and processed for DNA/RNA isolations as well as metabolomics or pharmacological/electrophysiological tests. Whole animals were used for all in situ hybridization and immunohistochemical tests as described35. Genomic DNA (gDNA) was isolated using Genomic-tip (QIAGEN) and total RNA was extracted using RNAqueous-Micro (Ambion/Life Technology) or RNAqueous according to manufacturers recommendations. Quality and quantity of gDNA was analysed on a Qubit2.0 Fluorometer (Life Technologies) and for RNA we used a 2100 Bioanalyzer (Agilent Technologies). For all details see Supplementary Methods sections 1.11.3.

All genomic sequence data for de novo assembly were generated on Roche 454 Titanium and Illumina Genome Analyzer IIx, HiSeq2000 and MiSeq instruments using both shotgun pair-end and mate-pair sequencing libraries with 39 kb inserts as summarized in Supplementary Tables 1 and 2. Shotgun sequencing was performed from a single individual. Owing to a limited amount of starting gDNA, mate pair libraries were constructed from 1012 individuals. In total, the genome sequencing is composed of 132,015,600,107 bp or ~132 Gb of data, which corresponds to 733825 physical coverage of the Pleurobrachia genome (the size of the P. bachei genome is estimated to be ~160180Mb); see Supplementary Methods sections 1.42.1.2.

The Pleurobrachia bachei draft genome was assembled using a custom approach designed to leverage the individual strengths of three popular de novo assembly packages and strategies: Velvet36, SOAPdenovo37, and pseudo-454 hybrid assembly with ABySS38. First, using filtered and corrected data, we performed individual assemblies from 454 and Illumina reads by the Newbler (Roche, Inc.) software. Then the merged/hybrid assembly was achieved using three individual assemblies (SOAPdenovo, Velvet and ABySS/Newbler as described in Supplementary Methods 2.2). Three gene model predictions were performed by Augustus39 and Fgenesh predictions with the Softberry Inc. Fgenesh++ pipeline40, 41 to incorporate information from full-length cDNA alignments and similar proteins from the eukaryotic section of the NCBI NR database42. After initial gene predictions in each of the three sets of genomic scaffolds, we screened each set of gene models for internal redundancy with the BLASTP program from NCBIs BLAST+ software suite43. A model was considered redundant if it: had 90% identity to other model; the alignment between the two models had a bit score of at least 100; and the model was shorter than the other model.

Scaffolds producing these gene models were pooled and then screened for prokaryotic contamination using UCSCs BLAT software package44 to produce the draft genome assembly version 1.0 (statistics can be found in Supplementary Table 5 and Supplementary Methods 2).

For annotation, gene models were uploaded to the In-VIGO BLAST interface, a blastp alignment of gene models was performed against the entirety of NCBIs non-redundant protein database and the Swiss-Prot protein database, and subsequently annotated in terms of Gene Ontology and KEGG pathways as well as Pfam domain identification. Transposable elements (TEs) were identified using not only WU-BLAST and its implementation in CENSOR but also databases for all known classes, superfamilies and clades of TEs described in the literature and/or collected in Repbase45. Detected sequences have been clustered based on their pairwise identities by using BLASTclust. All autonomous non-LTR retrotransposons have been classified based on RTclass1 (ref. 46). To merge partially predicted, non-redundant gene models with assembled transcriptome data, a custom Java tool was developed. This Java tool extended partial gene model predictions based on using transcriptome sequences to bridge 5 and 3 fragments of partially predicted genes. Using this Java tool, analysis of alignments of non-redundant gene models to assembled Pleurobrachia transcriptomes resulted to 19,523 (Supplementary Table 30) gene models. These gene models were used to also identify their possible homologues in assembled transcriptomes from 10 other ctenophore species sequenced (Supplementary Tables 10 and 11). All genomic sequences were submitted to NCBI on SRA accession number Project SRP001155 (Supplementary Methods 3.13.2).

Three sequencing technology platforms were used for transcriptome profiling (RNA-seq): Roche 454 Titanium, Illumina HiSeq2000 and Ion Proton/PGM (Ion Torrent, Life Technologies). RNA-seq was performed from all major embryonic and developmental stages (1 cell, 2 cells, 4 cells, 8 cells, 16 cells, 32 cells, 64 cells, early and later gastrula, 1 day and 3 day larvae), major adult tissues and organs (combs, mouth, tentacles, stomach, the aboral organ, body walls), and whole body of Pleurobrachia bachei. We developed a reduced representation sequencing protocol for the 454 and Ion Torrent sequencing platforms that can detect low abundance transcripts47. The method reduces the amount of sequencing and gives more accurate quantification and additional details of the procedure are reported elsewhere47, 48. In summary, we have generated 499,699,347 reads or ~47.9 Gb to achieve approximately 2,000 coverage of the Pleurobrachia transcriptome.

In addition, Illumina HiSeq sequencing was also performed with RNA extracted from the following ctenophore species: Euplokamis dunlapae, Coeloplana astericola, Vallicula multiformis, Pleurobrachia pileus, Pleurobrachia sp. (collected from the Middle Atlantic and later identified as a subspecies of P. pileus), Dryodora glandiformis, Beroe abyssicola, Mnemiopsis leidyi, Bolinopsis infundibulum and an undescribed species which belongs to the family Mertensiidae (Supplementary Table 3). Each sequencing project was individually assembled using the Trinity de novo assembly package49 and in selected cases using MIRA. Reads from developmental stages were also assembled using the CLCBio Genomics Workbench. Before each assembly, reads were quality trimmed and had adaptor contamination removed with cutadapt50. Full summaries of the transcriptome assemblies are presented in Supplementary Tables 4 and 10. Each transcriptome was mapped to the Pleurobrachia genome, and aligned to both NCBIs non-redundant protein database (NR) and the UniProtKB/Swiss-Prot (SP) protein database. Gene Ontology51 and Kyoto Encyclopedia of Genes and Genomes52, 53 (KEGG) terms were associated with each transcript. By first translating transcripts in all six reading frames, Pfam/SMART domains54 were assigned to each reference transcriptome.

Each reference transcriptome and its full set of annotation and expression data was uploaded to our transcriptome database http://moroz.hpc.ufl.edu/slimebase2/browse.php for downstream analysis and visualization55, 56. The database is integrated with UCSC type genome browser. Via the genome project homepage (http://neurobase.rc.ufl.edu/Pleurobrachia) all data sets have direct download options. Quantification of gene expression profiling was performed on all transcriptional data as described in Supplementary Methods 4.4. Hierarchical clustering was performed by Spotfire agglomerative algorithm. All primary transcriptome data was submitted to NCBI on SRA accession number Project SRP000992. (See Supplementary Methods 4.14.2.3 for details.)

To reconstruct basal metazoan phylogeny (see controversies in10, 11, 12, 13, 14, 15, 57), we conducted two sets of phylogenomic analysis using tools described elsewhere58. All analyses included new data from Pleurobrachia bachei and the sponges Sycon (Calcarea) and Aphrocallistes (Hexactinellida). For the first set of analyses, Ctenophora was represented by two species of Pleurobrachia and Mnemiopsis leidyi. Initial analyses included the taxa in Supplementary Table 12. For a subsequent analysis, sampling within Ctenophora was expanded to include ten additional taxa, each represented by a relatively deeply sequenced Illumina transcriptome (Supplementary Table 13). In order to reduce noise in the phylogenetic signal, we used strict criteria to exclude paralogues, highly derived sequences, mistranslated sequence regions, and ambiguously aligned positions in sequence alignments. Analyses were conducted in RAxML 7.2.7 (refs 59) using maximum likelihood (ML) with the CAT +WAG + F model. Topological robustness (that is, nodal support) for all ML analyses was assessed with 100 replicates of nonparametric bootstrapping. Details of phylogenomic analyses are presented in Supplementary Methods 7. ShimodairaHasegawa test17 was implemented in RAxML with the PROTGAMMAWAGF model17.

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The ctenophore genome and the evolutionary origins of neural systems

The genome of the termite reveals several clues about the insects' complex social structures, say scientists.

The genome of the termite has just been sequenced, and it is revealing several clues about how the pests create their rigid social order.

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For instance, the new genome, detailed today (May 20) in the journal Nature Communications, uncovers some of the underpinnings of termites' caste system, as well as the roots of the males' sexual staying power.

Like othersocial insects such as ants, honeybees and some wasps termites live in highly structured "caste systems," with each creature programmed to perform a rigidly defined job. A select few termite kings and queens reproduce, while drones and soldiers work, defend the colony or care for young. [Image Gallery: Ants of the World]

Yet termites evolved their social structure independently from ants and bees, which belong to an order known as Hymenoptera.

To understand how this happened, Jrgen Liebig, a behavioral biologist at Arizona State University, and his colleagues collected dampwood termites(Zootermopsis nevadensis nuttingi)that lived in Monterey, California. The researchers then sequenced the genome of the insects and measured how those genes were expressed, or turned on and off.

The research revealed several insights about termite sexual and social behavior.

Termite society is roughly half males and half females. Termites have sexually active kings as well as queens, and kings make sperm throughout their lifetimes. Dampwood termite males also have testes that shrivel and grow seasonally.

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Scientists unravel termite's genetic code. What did they learn?

May 21, 2014

Image Caption: Michael Scharf eyes a group of eastern subterranean termites, destructive pests in Indiana and the Eastern U.S. Credit: Purdue University photo / Tom Campbell

Brett Smith for redOrbit.com Your Universe Online

A large international team of researchers has announced the successful sequencing of the Nevada dampwood termite genome, according to a new study in Nature Communications.

The study team said that not only is the genome crucial for understanding the social insect, it also provides information that could be used for more effective pest control.

The termite genome reveals many unique genetic targets that can be disrupted for better termite control, said Michael Scharf, an entomology professor at Purdue University, in a statement. Depending on which gene or protein that is targeted, we could disrupt termites neurological processes, molting, digestive factors or cuticle formation. Were just limited by our imagination.

While Nevada dampwood termites dont cause substantial damage to buildings, they are closely associated with other major pests such as the eastern subterranean termite, which is the predominant pest in the Central and the Eastern US.

Termites cause an estimated $40 billion in damage and control costs each year the study team said. The pests are typically controlled using chemicals, which often leach into the ground and affect other organisms.

While current pesticides are very effective products, the problem is that youre injecting large volumes of them into the soil around the house, Scharf said. It would be nice to move to a greener technology, and thats what the genome sequence could enable us to do.

He went on to say small amounts of treated timber, which could be shared with the colony, might be used to bait termites. Newer innovations such as gene silencing could also be used to eliminate the pests. Gene silencing methods might target essential bits of RNA necessary for the insects survival.

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Termite Genome Sequenced, Could Lead To More Effective Pest Control Methods In The Future

Leonid L. Moroz/Mathew Citarella

Pleurobrachia bachei lacks many common genes.

Comb jellies, or ctenophores, look like tiny disco balls and propel themselves around oceans using specialized hairs, lapping up small prey with their sticky tentacles. They are aliens whove come to Earth, says Leonid Moroz, a neuroscientist at the University of Florida in St Augustine.

The genome of the Pacific sea gooseberry (Pleurobrachia bachei), which Moroz and his team report online today in Nature, adds to the mystery of ctenophores (L. L. Moroz etal. Nature http://dx.doi.org/10.1038/nature13400; 2014). The sequence omits whole classes of genes found in all other animals, including genes normally involved in immunity, development and neural function. For that reason, the researchers contend that ctenophores evolved a nervous system independently.

Ctenophores have long vexed taxonomists. Their resemblance to jellyfish earned them a spot on the tree of life as a sister group to cnidarians (the phylum that includes jellyfish). On the basis of their nervous systems which can detect light, sense prey and move musculature many researchers had them branching off from the common ancestor of other animals after the sponges and flattened multicellular blobs known as placozoans, neither of which have a nervous system. Now armed with data showing that ctenophores lack many common genes, some scientists contend that these are the closest living relatives to the first animals.

Morozs team argues that the P.bachei genome, along with gene-expression data from other ctenophores, supports this theory. For example, microRNAs, which regulate gene expression in other animals, are completely missing from the sea gooseberry genome.

Leonid Moroz and Andreas Hejnol discuss the comb jelly genome

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The biggest surprise, Moroz says, was the absence of many standard components of a nervous system. Nearly all known nervous systems use the same ten primary neurotransmitters; the Pacific sea gooseberry seems to employ just one or two. Moroz speculates that the organism might complete its nervous system using molecules that researchers have not yet found in this species, such as specialized protein hormones.

The uniqueness of this ctenophores nervous system leads Moroz and his team to argue that it must have evolved independently, after the ctenophore lineage branched off from other animals some 500million years ago. Everyone thinks this kind of complexity cannot be done twice, Moroz says. But this organism suggests that it happens.

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Jelly genome mystery

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20-May-2014

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

Like ants and honey bee, termites are also eusocial insects. In colonies of termites, only a few individuals have reproductive ability (called queens and kings), while other individuals perform non-reproduction tasks like foraging, brood care or defence (called workers and soldiers). Living in societies has helped termites adapt to their environments and contributed to their ecological success. As major detritivores, termites play pivotal roles in maintaining biodiversity, particularly in tropical habitats. On the other hand, termite are considered as major pests of human structures, with an annual worldwide cost in damage and control estimated at US$40 billions

Although sharing many similarities with ants and honey bee, which belong to Hymenoptera and have the unique haplodiploidy sex determination system, termites evolved the eusociality in a distantly related order called Isoptera. Termites also exhibit different pattens regarding sociality compared to social Hymenopterans. For instance, the kings of termites, which are long-term male reproductives and have the same status as the queens, are absent in social Hymenopterans. Therefore termites are a highly valuable system for studying social evolution. By far 10 social Hymenopteran genomes (8 ants and 2 bees) have been published, but no termite genome has been published yet. In a study published online today in Nature Communications, researchers from China, America and Germany have reported the sequences and analyses of the first termite genome (Zootermopsis nevadensis), revealing new insights into the molecular underpinning of complex societies in termites.

Z. nevadensis belongs to the family of dampwood termites (Termopsidae) which are rather basal termite species. Z. nevadensis has the smallest genome size known among termites (only about 500Mb), which is beneficial to building the assembly with short sequencing reads. In addition to the genomic data, the researchers also generated transcriptomic data for 25 samples, representing different sexes, developmental stages and castes, for functional genomics.

"One of the major findings in our study is that, we found four gene families involved in spermatogenesis, have specifically expanded in the termite genome, and from the transcriptome data we also observed up-regulated expression of these genes in male reproductive individuals" said Cai Li, one of the lead co-authors of this project. "This is very interesting, because in a termite colony queens and kings mate repeatedly during their long lives, while in the eusocial Hymenopterans, the reproduction system is usually queen-centralized and single-time mating. Our findings shed light on the molecular explanations for such difference, though a full understanding about this still need further work."

Compared to other insect genomes, Z. nevadensis have a considerably different repertoire of chemoreceptor genes, the important components in sensory systems of insects. Z. nevadensis has much fewer odorant receptors (ORs), which were found expanded in ants and honey bee. However, the ionotropic receptor (IR) family has expanded largely in termite. "The lower number of olfactory receptors reflects this termite's lifestyle. Z. nevadensis is a basal termite, living their entire lives within a single log. Most of the ants and the honey bee show sophisticated communication behaviour and nestmate recognition and need more ORs to discriminate volatile substances and communicate with conspecifics. However, we predict the'higher' termites, with a more sophisticated division of labor, would show an increase in OR genes." Said Jrgen Liebig of Arizona State University, one of corresponding authors of this study.

By comparing with other eusocial insect genomes, the researchers also found some gene families (e.g. vitellogenins, cytochrome P450s and hexamerins) involved in caste differentiation and reproductive division of labour in social Hymenopteran insects show similar patterns in termites, suggesting convergent evolution of these regulatory mechanisms.

"This first termite genome represents an important step, because it fills a big gap in social insect genomics. It has been a puzzle for a long time that if there is any common mechanism leading to the development of eusociality in different eusocial insect groups. We found several regulatory factors like vitellogenins, juvenile hormone et al. displaying significantly gene expression changes among castes of termite. Similar patterns were also observed in other eusocial insects before." Said Guojie Zhang of China National Genebank, another corresponding author of this study, 'With more and more social insect genomes available, we can have a closer look at this question with comparative genomic analyses among different social insect groups and will hopefully get a more thorough understanding of social evolution'

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The first termite genome fills a gap in social inset genomics

What Is Genome Sequencing?
How Do We Assemble Genomes? (Part 2/12)

By: Bioinformatics Algorithms: An Active Learning Approach

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What Is Genome Sequencing? - Video

[14.05.20] Park Jung Min attends #39;Genome Hazard() #39; VIP Movie Premiere
Credit: http://www.obsnews.co.kr/news/articleView.html?idxno=806144.

By: Sakura Dream

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[14.05.20] Park Jung Min attends 'Genome Hazard()' VIP Movie Premiere - Video

cre-lox and cre recombinases in Mouse Genome Informatics: worksheet module 2
This video is an introduction to the cre-lox system of conditional mouse genetic engineering and tools available in the Mouse Genome Informatics database, fo...

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cre-lox and cre recombinases in Mouse Genome Informatics: worksheet module 2 - Video

The social structure of termites evolved independently from bees and ants, but all the species seem to share similar chemical tags that control a few genes

This image shows various castes of the termite Zootermopsis nevadensis: a soldier (with large dark head), a neotenic reproductive (darker individual without enlarged head), several larval instars (lighter individuals), and a nymph (light individual with darker wing buds) Liebig et al

The genome of the termite has just been sequenced, and it is revealing several clues about how the pests create their rigid social order.

For instance, the new genome, detailed today (May 20) in the journal Nature Communications, uncovers some of the underpinnings of termites' caste system, as well as the roots of the males' sexual staying power.

Social bugs

Like other social insects such as ants, honeybees and some wasps termites live in highly structured "caste systems," with each creature programmed to perform a rigidly defined job. A select few termite kings and queens reproduce, while drones and soldiers work, defend the colony or care for young. [Image Gallery: Ants of the World]

Yet termites evolved their social structure independently from ants and bees, which belong to an order known as Hymenoptera.

To understand how this happened, Jrgen Liebig, a behavioral biologist at Arizona State University, and his colleagues collected dampwood termites(Zootermopsis nevadensis nuttingi) that lived in Monterey, California. The researchers then sequenced the genome of the insects and measured how those genes were expressed, or turned on and off.

Sex differences

The research revealed several insights about termite sexual and social behavior.

Read more from the original source:
Termite Genome Reveals Details of "Caste System"