Hermansen Russell A, Oswald Benjamin P, Knight Stormy, Shank Stephen D, Northover David, Korunes Katharine L, Michel Stephen N, Liberles David A
Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
J Mol Evol. 2017 Aug;85(1-2):46-56. doi: 10.1007/s00239-017-9806-8. Epub 2017 Aug 9.
With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context. Gene families include alignments, phylogenetic trees, lineage-specific dN/dS ratios, reconciliation with the species tree to enable both the mapping and the identification of duplication events, mapping of gene families onto pathways, and mapping of amino acid substitutions onto protein structures. In addition to organization of the data, new phylogenetic visualization tools have been developed to aid in interpreting the data that are also available, including TreeThrasher and TAED Tree Viewer. A new resource of gene families organized by species and taxonomic lineage promises to be a valuable comparative genomics database for molecular biologists, evolutionary biologists, and ecologists. The new visualization tools and database framework will be of interest to both evolutionary biologists and bioinformaticians.
随着基因和基因组序列的大量积累，需要生成经过整理的比较基因组数据库，以便在进化背景下解释结果。这些资源有助于在映射到系统发育树上的基因组、蛋白质结构以及通路内相互作用的背景下理解基因的共同进化。本文介绍了一个系统发育索引基因家族数据库——适应性进化数据库（TAED），它在物种树背景下组织基因家族及其进化历史。基因家族包括比对、系统发育树、特定谱系的dN/dS比率、与物种树的比对以实现重复事件的映射和识别、基因家族在通路上的映射以及氨基酸取代在蛋白质结构上的映射。除了数据组织，还开发了新的系统发育可视化工具来辅助解释现有数据，包括TreeThrasher和TAED树查看器。一个按物种和分类谱系组织的基因家族新资源有望成为分子生物学家、进化生物学家和生态学家的宝贵比较基因组数据库。新的可视化工具和数据库框架将引起进化生物学家和生物信息学家的兴趣。
