Reconstruction of ancient genome and gene order from complete microbial genome sequences |
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Authors: | Wang Yuhong Li Wei Zhang Tongtong Ding Chuanfang Lu Zhibin Long Nanye Rose John P Wang Bi-Cheng Lin Dawei |
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Institution: | Department of Molecular Biology, Jilin University, Changchun 130023, PR China. yuhong_wang@yahoo.com |
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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. |
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Keywords: | Microbial genome sequences Travel salesman problem Random cost algorithm Global optimization Genome evolution |
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