OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis.
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis.
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DOI：
10.1186/s12864-016-2886-9
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发表时间：
2016-08-25
期刊：
影响因子：
4.4
通讯作者：
Colbourne JK
中科院分区：
文献类型：
--
作者：
Rago A;Gilbert DG;Choi JH;Sackton TB;Wang X;Kelkar YD;Werren JH;Colbourne JK
丽蝇蛹集茧蜂是一种新的单倍二倍体模式昆虫。它在昆虫遗传学的比较、进化和行为遗传学研究中占有重要地位。N. 2010年发表了丽翅虫和两个姊妹种的基因组数据，但此后已经产生了大量的转录组数据，从而能够改进原始（OGS1.2）注释的基因集。我们描述并应用EvidentialGene方法来产生更新的基因集（OGS 2）。我们还进行了比较分析，展示了修订后的注释基因集的有用性。修订后的注释（OGS 2）现在由24，388个基因组成，与OGS1.2的18，850个相比。改进包括97%的基因的非翻译区（UTR）的几乎完整的注释，而OGS1.2的基因只有28%。在这个最新的基因组中，RNA-Seq验证的内含子的分数也从85%增长到98%。EST和RNA-Seq表达数据为4146个基因的几个非蛋白质编码位点和7712个替代转录本提供了支持。值得注意的是，我们报告180个基因萝拉替代转录。Nasonia现在拥有最完整的昆虫基因组;只有27个保守的单拷贝直系同源物在节肢动物中从OGS 2中缺失。它的基因组还包含2.1倍的重复基因和1.4倍的单拷贝基因比果蝇基因组。Nasonia的基因数量比其他已测序的hyperteran物种要大，这是由于基因组注释的改进和黄蜂谱系中的独特基因。我们确定了1008个基因和171个基因家族，分别在蛋白质进化速率和重复历史上显著偏离其他hyperterans。我们还提供了一个分析的选择性剪接，揭示了基因与没有注释的异构体的特点是较短的成绩单，较少的内含子，更快的蛋白质进化和更高的概率复制比基因有选择性的成绩单。全基因组表达数据极大地改进了N.通过增加基因计数，减少缺失基因的数量，并提供有关剪接和基因结构的更全面数据，改进的基因集识别了与Nasonia生物学相关的谱系特异性基因组特征，以及许多新基因。OGS 2及其相关搜索工具可在http：//arthropods.eugenes.org/EvidentialGene/nasonia/、www.hymenopteragenome.org/nasonia/和waspAtlas：www.tinyURL.com/waspAtlas上查阅。EvidentialGene管道可在https://sourceforge.net/projects/evidentialgene/上获得。本文的在线版本（doi：10.1186/s12864-016-2886-9）包含补充材料，可供授权用户使用。
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. 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. 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/. The 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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影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1126/science.1197761
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Colbourne JK;Pfrender ME;Gilbert D;Thomas WK;Tucker A;Oakley TH;Tokishita S;Aerts A;Arnold GJ;Basu MK;Bauer DJ;Cáceres CE;Carmel L;Casola C;Choi JH;Detter JC;Dong Q;Dusheyko S;Eads BD;Fröhlich T;Geiler-Samerotte KA;Gerlach D;Hatcher P;Jogdeo S;Krijgsveld J;Kriventseva EV;Kültz D;Laforsch C;Lindquist E;Lopez J;Manak JR;Muller J;Pangilinan J;Patwardhan RP;Pitluck S;Pritham EJ;Rechtsteiner A;Rho M;Rogozin IB;Sakarya O;Salamov A;Schaack S;Shapiro H;Shiga Y;Skalitzky C;Smith Z;Souvorov A;Sung W;Tang Z;Tsuchiya D;Tu H;Vos H;Wang M;Wolf YI;Yamagata H;Yamada T;Ye Y;Shaw JR;Andrews J;Crease TJ;Tang H;Lucas SM;Robertson HM;Bork P;Koonin EV;Zdobnov EM;Grigoriev IV;Lynch M;Boore JL
通讯作者：
Boore JL
影响因子：
4.4
作者：
Eckalbar WL;Hutchins ED;Markov GJ;Allen AN;Corneveaux JJ;Lindblad-Toh K;Di Palma F;Alföldi J;Huentelman MJ;Kusumi K
通讯作者：
Kusumi K
影响因子：
30.8
作者：
Ayroles, Julien F.;Carbone, Mary Anna;Stone, Eric A.;Jordan, Katherine W.;Lyman, Richard F.;Magwire, Michael M.;Rollmann, Stephanie M.;Duncan, Laura H.;Lawrence, Faye;Anholt, Robert R. H.;Mackay, Trudy F. C.
通讯作者：
Mackay, Trudy F. C.
影响因子：
64.8
作者：
Bordenstein, SR;O'Hara, FP;Werren, JH
通讯作者：
Werren, JH