Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

BMC Bioinformatics

Research Article

Youjun Wang¹  Sisi Zheng¹  Nhung Nguyen²  Yubin Zhou²  Jia Song³  Kui Lin³ 

[1] Beijing Key Laboratory of Gene Resources and Molecular Development College of Life Sciences, Beijing Normal University, 100875, Beijing, China;Center for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University, 77030, Houston, TX, USA;MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875, Beijing, China;

关键词: Evolutionary history;    Gene family;    Phylogenetic tree;    STIMATE;    Chordate;   

DOI  :  10.1186/s12859-017-1850-2

 received in 2017-04-17, accepted in 2017-09-26,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundBecause phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method.ResultsOn the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes.ConclusionsBy integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

【 授权许可】

CC BY   
© The Author(s). 2017