An evolutionarily and ecologically focused strategy for genome sequencing efforts

Barribeau, Seth M.

doi:10.1038/hdy.2011.109

Cited by 1 publication

(1 citation statement)

References 18 publications

(16 reference statements)

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“…In the coming years, projects such as the i5K and 1KITE [ 5 ] will continue to deliver new insect genomes and transcriptomes to the research community, with the goal of improving genomic knowledge for this most speciose animal clade [ 17 ]. Expanding the taxonomic breadth and number of well annotated genomes is important to develop new research avenues, and several quality measures are necessary for the accurate interpretation of comparative genomic, transcriptomic and epigenomic data [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

et al. 2016

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BackgroundNasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N. vitripennis and two sibling species were published in 2010, yet a considerable amount of transcriptiome data have since been produced thereby enabling improvements to the original (OGS1.2) annotated gene set. We describe and apply the EvidentialGene method used to produce an updated gene set (OGS2). We also carry out comparative analyses showcasing the usefulness of the revised annotated gene set.ResultsThe revised annotation (OGS2) now consists of 24,388 genes with supporting evidence, compared to 18,850 for OGS1.2. Improvements include the nearly complete annotation of untranslated regions (UTR) for 97 % of the genes compared to 28 % of genes for OGS1.2. The fraction of RNA-Seq validated introns also grow from 85 to 98 % in this latest gene set. The EST and RNA-Seq expression data provide support for several non-protein coding loci and 7712 alternative transcripts for 4146 genes. Notably, we report 180 alternative transcripts for the gene lola.Nasonia now has among the most complete insect gene set; only 27 conserved single copy orthologs in arthropods are missing from OGS2. Its genome also contains 2.1-fold more duplicated genes and 1.4-fold more single copy genes than the Drosophila melanogaster genome. The Nasonia gene count is larger than those of other sequenced hymenopteran species, owing both to improvements in the genome annotation and to unique genes in the wasp lineage.We identify 1008 genes and 171 gene families that deviate significantly from other hymenopterans in their rates of protein evolution and duplication history, respectively. We also provide an analysis of alternative splicing that reveals that genes with no annotated isoforms are characterized by shorter transcripts, fewer introns, faster protein evolution and higher probabilities of duplication than genes having alternative transcripts.ConclusionsGenome-wide expression data greatly improves the annotation of the N. vitripennis genome, by increasing the gene count, reducing the number of missing genes and providing more comprehensive data on splicing and gene structure. The improved gene set identifies lineage-specific genomic features tied to Nasonia’s biology, as well as numerous novel genes.OGS2 and its associated search tools are available at http://arthropods.eugenes.org/EvidentialGene/nasonia/, www.hymenopteragenome.org/nasonia/ and waspAtlas: www.tinyURL.com/waspAtlas.The EvidentialGene pipeline is available at https://sourceforge.net/projects/evidentialgene/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2886-9) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%