Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification. To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian inference with training models for nucleotide composition. Our method gives the average posterior probability (horizontal transfer index) for each gene sequence, with a low horizontal transfer index indicating recent horizontal transfer. We found that 14% of open reading frames in 116 prokaryotic complete genomes were subjected to recent horizontal transfer. Based on this data set, we quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions. Thus, the transferability of genes seems to depend heavily on their functions.
Bibliographical noteFunding Information:
We thank N. Tsuboi for coding the horizontally transferred gene detection programs; N. Nishinomiya, M. Matsuo and R. Yamaguchi for technical assistance; and K. Ikeo, J.S. Hwang and R. Barrero for their comments and suggestions. T.I. and T.G. were supported in part by grants from the New Energy and Industrial Technology Development Organization and the Ministry of Economy, Technology, and Industry of Japan. T.I., T.G. and H.M. were supported by grants from the Ministry of Education, Sports, Culture, Science and Technology of Japan.
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