Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.
Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.
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DOI：
10.1016/j.cub.2022.04.085
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发表时间：
2022-06-20
期刊：
影响因子：
9.2
通讯作者：
Eddy, Sean R.
中科院分区：
文献类型：
--
作者：
Weisman, Caroline M.;Murray, Andrew W.;Eddy, Sean R.
不同物种的基因组比较被用来识别谱系特异性基因，这些基因对一个物种或进化枝来说是独特的。谱系特异性基因通常被认为代表了遗传上的新奇，是独特适应的基础。这些基因的鉴定不仅依赖于基因组序列，还依赖于推断的基因注释。比较分析通常使用已使用不同方法注释的可用基因组，增加了正向DNA序列可能被错误地注释为一个物种而不是另一个物种的基因的风险，从而出现谱系特异性。为了评估这种“注释异质性”的影响，我们确定了四个进化枝的物种与测序的基因组与一个以上的公开可用的基因注释，使我们能够比较的谱系特异性基因的数量时，推断不同的注释方法使用的注释方法是统一的进化枝。在这些案例研究中，注释异质性增加了谱系特异性基因的表观数量高达15倍，这表明注释异质性是潜在伪影的重要来源。
Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage-specific as a result. To evaluate the impact of such “annotation heterogeneity,” we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.
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影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
14.9
作者：
Larkin A;Marygold SJ;Antonazzo G;Attrill H;Dos Santos G;Garapati PV;Goodman JL;Gramates LS;Millburn G;Strelets VB;Tabone CJ;Thurmond J;FlyBase Consortium
通讯作者：
FlyBase Consortium
影响因子：
7.7
作者：
James JE;Willis SM;Nelson PG;Weibel C;Kosinski LJ;Masel J
通讯作者：
Masel J
影响因子：
3.3
作者：
Casola C
通讯作者：
Casola C
影响因子：
4.4
作者：
Neme R;Tautz D
通讯作者：
Tautz D