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  Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

Athanasouli, M., Witte, H., Weiler, C., Loschko, T., Eberhardt, G., Sommer, R., & Rödelsperger, C. (2020). Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics, 21(1):. doi:10.1186/s12864-020-07100-0.

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アイテムのパーマリンク: https://hdl.handle.net/21.11116/0000-000A-547F-A 版のパーマリンク: https://hdl.handle.net/21.11116/0000-000F-3EC9-A
資料種別: 学術論文

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 作成者:
Athanasouli, M1, 著者           
Witte, H1, 著者           
Weiler, C1, 2, 著者           
Loschko, T1, 著者           
Eberhardt, G1, 著者           
Sommer, RJ1, 著者           
Rödelsperger, C1, 著者           
所属:
1Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375786              
2Entomo-Nematology Group, Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3507713              

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 要旨: Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics.
Results: Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%.
Conclusions: Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

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 日付: 2020-10
 出版の状態: 出版
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 識別子(DOI, ISBNなど): DOI: 10.1186/s12864-020-07100-0
PMID: 33045985
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出版物名: BMC Genomics
種別: 学術雑誌
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出版社, 出版地: BioMed Central
ページ: 9 巻号: 21 (1) 通巻号: 708 開始・終了ページ: - 識別子(ISBN, ISSN, DOIなど): ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010