AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution
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DOI：
10.1093/database/baz022
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发表时间：
2019-03-20
影响因子：
5.8
通讯作者：
Mahadevan, Radhakrishnan
中科院分区：
文献类型：
--
作者：
Correia, Kevin;Yu, Shi M.;Mahadevan, Radhakrishnan
芽殖酵母通过利用各种代谢特征栖息在一系列环境中。这些性状的遗传基础大多是未知的，因此无法在代谢工程的底盘生物体中添加或去除它们。深入了解酵母泛基因组中直向同源物、旁系同源物和异种同源物的进化可以帮助弥合这些基因型；然而，现有的系统发育数据库并不涵盖不同的酵母，有时无法区分这些同源物。为了帮助了解酵母中这些性状的分子进化，我们创建了通过重建同源祖先分析酵母 (AYbRAH)，这是一个开源数据库，包含 Dikarya 33 种不同真菌和酵母的预测和手动管理的直向同源群，跨越 6 亿年的进化。 OrthoMCL和OrthoDB分别用于将蛋白质序列聚类为直向同源物和同源物组； MAFFT 和 PhyML 重建了所有同源群的系统发育。将酶和小代谢物转运蛋白的直系同源分配与其系统发育重建进行比较，并进行策划以解决任何差异。有关同源物和直系同源物组的信息可以在 AYbRAH 门户网站 (https://lmse.github.io/aybrah/) 中查看，包括功能注释、线粒体定位和跨膜域预测、文献参考和系统发育重建。 AYbRAH 中的直系同源分配与 HOGENOM、KEGG Orthology、OMA、eggNOG 和 PANTHER 进行了比较。 PANTHER 和 OMA 与 AYbRAH 具有最一致的直系同源群体，而其他系统发育数据库则具有大量的蛋白质聚类不足、过度聚类或无直系同源注释。讨论了 AYbRAH 的未来计划，并向其他寻求创建精选直向同源数据库的研究社区提出了建议。数据库 URL：https://lmse.github.io/aybrah/
Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these genotypes; however, existing phylogenomic databases do not span diverse yeasts, and sometimes cannot distinguish between these homologs. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML reconstructed the phylogeny of all homolog groups. Ortholog assignments for enzymes and smallmetabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://lmse.github.io/aybrah/), including functional annotations, predictions for mitochondrial localization and transmembrane domains, literature references and phylogenetic reconstructions. Ortholog assignments in AYbRAH were compared to HOGENOM, KEGG Orthology, OMA, eggNOG and PANTHER. PANTHER and OMA had the most congruent ortholog groups with AYbRAH, while the other phylogenomic databases had greater amounts of under-clustering, over-clustering or no ortholog annotations for proteins. Future plans are discussed for AYbRAH, and recommendations are made for other research communities seeking to create curated ortholog databases.Database URL: https://lmse.github.io/aybrah/