GeneSeqToFamily - Species Tree

Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.

基因重复是推动演化创新的核心因素之一，基因家族的收缩与扩张通常与形态、生理及环境适应密切相关。同源基因研究有助于解析基因家族的演化历程，其在追溯祖先基因重复事件、鉴定受正向选择且源自共同祖先的分化基因方面发挥关键作用。目前已有多款工具可用于基因家族鉴定与物种间共线性信息可视化，例如MSOAR、OrthoMCL及HomoloGene，能够从家族层面展现共线性区域的演化概览。但遗憾的是，此类工具均未提供基因内部结构变化的相关信息，例如多基因组间祖先外显子边界的保守性情况。Ensembl GeneTrees计算流程则基于编码序列生成基因树，并提供外显子保守性的详细信息，该流程被应用于Ensembl Compara项目以开展基因家族发现工作。