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

Rago, Alfredo LU ; Gilbert, Donald G; Choi, Jeong-Hyeon; Sackton, Timothy B; Wang, Xu; Kelkar, Yogeshwar D; Werren, John H and Colbourne, John K (2016) In BMC Genomics 17.
Abstract

Nasonia 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.

RESULTS: The revised annotation (OGS2) now consists of 24,388 genes with supporting evidence, compared to 18,850 for... (More)

Nasonia 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.

RESULTS: The 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.

CONCLUSIONS: Genome-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/ .

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keywords
Alternative Splicing, Animals, Computational Biology, Contig Mapping, Databases, Nucleic Acid, Evolution, Molecular, Gene Expression Profiling, Genes, Insect, Genome, Insect, Genome-Wide Association Study, Genomics, Molecular Sequence Annotation, Multigene Family, Open Reading Frames, RNA, Untranslated, Software, Wasps, Web Browser, Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, N.I.H., Extramural
in
BMC Genomics
volume
17
pages
25 pages
publisher
BMC Genomics
external identifiers
  • scopus:84983638238
ISSN
1471-2164
DOI
10.1186/s12864-016-2886-9
language
English
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no
id
6c7ebf4d-ff8b-4a1b-abeb-ec5409f7e31c
date added to LUP
2018-01-15 13:26:25
date last changed
2019-03-19 03:47:34
@article{6c7ebf4d-ff8b-4a1b-abeb-ec5409f7e31c,
  abstract     = {<p>Nasonia 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.</p><p>RESULTS: The 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.</p><p>CONCLUSIONS: Genome-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/ .</p>},
  articleno    = {17:678},
  author       = {Rago, Alfredo and Gilbert, Donald G and Choi, Jeong-Hyeon and Sackton, Timothy B and Wang, Xu and Kelkar, Yogeshwar D and Werren, John H and Colbourne, John K},
  issn         = {1471-2164},
  keyword      = {Alternative Splicing,Animals,Computational Biology,Contig Mapping,Databases, Nucleic Acid,Evolution, Molecular,Gene Expression Profiling,Genes, Insect,Genome, Insect,Genome-Wide Association Study,Genomics,Molecular Sequence Annotation,Multigene Family,Open Reading Frames,RNA, Untranslated,Software,Wasps,Web Browser,Journal Article,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, Non-P.H.S.,Research Support, N.I.H., Extramural},
  language     = {eng},
  month        = {08},
  pages        = {25},
  publisher    = {BMC Genomics},
  series       = {BMC Genomics},
  title        = {OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis},
  url          = {http://dx.doi.org/10.1186/s12864-016-2886-9},
  volume       = {17},
  year         = {2016},
}