From genome to life-style
One of the major goals of evolutionary biology is to understand the evolutionary mechanisms of adaptation. Bacteria are one of the most abundant life forms on earth and occupy all kinds of niches. The completion of a large number of bacterial genomes has offered an unprecedented opportunity to investigate the evolutionary changes that are critical to the adaptation of bacteria to their diverse environments. Here, we focus on identifying the genes and pathways that are essential to the different lifestyles a-proteobacteria. We first classify 64 α-proteobacteria with complete genomes into three lifestyle categories: animalassociated (29), plant-associated (11), and freeliving (24). We then construct a universal gene set and correlate the presence/ absence patterns of the genes with the life-styles of the host genomes with two complementary approaches. As the first approach, we construct an artificial neural network based life-style classifier using the presence/absence patterns of genes in different bacteria. The leave-oneout test shows that the classifier has an accuracy of 92.19% (i.e. 59/64). As the second approach, we map the presence and absence of genes to the phylogenetic tree of these bacteria and infer the gene gain and loss patterns with the small parsimony method. These results demonstrate that evolutionary changes in genes and pathways that are essential to the adaptation of bacteria can be identified through the comparative analysis of the whole genomes of bacteria with different lifestyles.
Zhaocheng Fan Jiayuan Zhao Xiaoyan Zhu Yang Zhong Renyi Liu Tao Jiang
State Key Laboratory on Intelligent Technology and Systems, Tsinghua National Laboratory for Informa Ministry of Education Key Laboratory for Siodiversity Science and Ecological Engineering, School of Departrnent of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA Department of Computer Science and Engineering, University of California at Riverside, Riverside, CA
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
901
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）