title: Reconstruction of ancient genome and gene order from complete microbial genome sequences.
abstract: Microbial genome sequences provide us with the fossil records for inferring their origination and evolution. Assuming that current microbial genomes are the evolutionary results of ancient genomes or fragments and the neighboring genes in ancient genomes are more likely neighbors in current genomes, in this paper we proposed a paleontological algorithm and assembled the orthologous gene groups from 66 complete and current microbial genome sequences into a pseudo-ancient genome, which consists of continuous fragments of various sizes. We performed bootstrap resampling and correlation analyses and the results showed that the assembled ancient genome and fragments are statistically significant and the genes of the same fragment are inherently related and likely derived from common ancestors. This method provides a new computational tool for studying microbial genome structure and evolution.
authors.affiliation: Department of Molecular Biology, Jilin University, Changchun 130023, PR China. yuhong_wang@yahoo.com
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Tongtong
authors.initials: T
authors.lastname: Zhang
authors.forename: Chuanfang
authors.initials: C
authors.lastname: Ding
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Lu
authors.forename: Nanye
authors.initials: N
authors.lastname: Long
authors.forename: John P
authors.initials: JP
authors.lastname: Rose
authors.forename: Bi-Cheng
authors.initials: BC
authors.lastname: Wang
authors.forename: Dawei
authors.initials: D
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D019143:Evolution, Molecular; D023061:Gene Order; D016680:Genome, Bacterial; D008957:Models, Genetic