Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence

doi:10.1016/S1671-2927(00)8618

Journal of Integrative Agriculture ›› 2012, Vol. 12 ›› Issue (6): 954-961.DOI: 10.1016/S1671-2927(00)8618

Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence

JIN Gu-lei, ZHANG Guo-qing, ZHU Jun, ZHOU Xue-ping, SUN Guo-chang, LI Bin, ZHU Bo

1.State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture/Institute of Biotechnology, Zhejiang University, Hangzhou 310029, P.R.China
2.Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, P.R.China
3.Crop Management Station, Jiaxing 314051, P.R.China
4.State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control/Institute of Plant Protection and Microbiology,Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R.China

收稿日期:2011-05-16 出版日期:2012-06-01 发布日期:2012-07-20
通讯作者: LI Bin, Tel: +86-571-88982412, E-mail: libin0571@zju.edu.cn; ZHU Bo, Tel: +86-571-88982412, E-mail:bzhu@zju.edu.cn
作者简介:JIN Gu-lei, E-mail: guleijin@zju.edu.cn
基金资助:
This project was supported by the Natural Science Foundation of Zhejiang Province of China (Y3090150), the Fundamental Research Funds for the Central Universities, China, the Zhejiang Provincial Project, China (2010R10091), the Research Project for Commonweal Industry of Agricultural Ministry, China (nyhyzx 201003029; 201003066), the Specialized Research Fund for the Doctoral Program of Higher Education, China (20090101120083), and the Key Subject Construction Program for Modern Agricultural Biotechnology and Crop Disease Control of Zhejiang, China.

Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence

JIN Gu-lei, ZHANG Guo-qing, ZHU Jun, ZHOU Xue-ping, SUN Guo-chang, LI Bin, ZHU Bo

1.State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture/Institute of Biotechnology, Zhejiang University, Hangzhou 310029, P.R.China
2.Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, P.R.China
3.Crop Management Station, Jiaxing 314051, P.R.China
4.State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control/Institute of Plant Protection and Microbiology,Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R.China

Received:2011-05-16 Online:2012-06-01 Published:2012-07-20
Contact: LI Bin, Tel: +86-571-88982412, E-mail: libin0571@zju.edu.cn; ZHU Bo, Tel: +86-571-88982412, E-mail:bzhu@zju.edu.cn
About author:JIN Gu-lei, E-mail: guleijin@zju.edu.cn
Supported by:
This project was supported by the Natural Science Foundation of Zhejiang Province of China (Y3090150), the Fundamental Research Funds for the Central Universities, China, the Zhejiang Provincial Project, China (2010R10091), the Research Project for Commonweal Industry of Agricultural Ministry, China (nyhyzx 201003029; 201003066), the Specialized Research Fund for the Doctoral Program of Higher Education, China (20090101120083), and the Key Subject Construction Program for Modern Agricultural Biotechnology and Crop Disease Control of Zhejiang, China.

摘要/Abstract

摘要： Horizontal gene transfer (HGT) plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and “leaves of the tree”. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.

关键词: Xanthomonas, core and pan-genome, gene gain/loss, horizontal gene transfer

Abstract: Horizontal gene transfer (HGT) plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and “leaves of the tree”. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.

Key words: Xanthomonas, core and pan-genome, gene gain/loss, horizontal gene transfer

JIN Gu-lei, ZHANG Guo-qing, ZHU Jun, ZHOU Xue-ping, SUN Guo-chang, LI Bin, ZHU Bo . Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence[J]. Journal of Integrative Agriculture, 2012, 12(6): 954-961.

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Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence

Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence

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