Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence
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 strain...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2012-06-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311912600860 |
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| author | Gu-lei JIN Guo-qing ZHANG Guan-lin XIE Jun ZHU Miao-miao LOU Xue-ping ZHOU Xiao-wei ZHANG Guo-chang SUN Bin LI Bo ZHU |
| author_facet | Gu-lei JIN Guo-qing ZHANG Guan-lin XIE Jun ZHU Miao-miao LOU Xue-ping ZHOU Xiao-wei ZHANG Guo-chang SUN Bin LI Bo ZHU |
| author_sort | Gu-lei JIN |
| collection | DOAJ |
| description | 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 1547 genes while the pan-genome will increase up to 22624 genes when sequencing 1000 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. |
| format | Article |
| id | doaj-art-5e71c12614ba4adc88c4ecb9c71e2e68 |
| institution | Kabale University |
| issn | 2095-3119 |
| language | English |
| publishDate | 2012-06-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-5e71c12614ba4adc88c4ecb9c71e2e682025-08-20T03:56:17ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192012-06-0111695496110.1016/S2095-3119(12)60086-0Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species DivergenceGu-lei JIN0Guo-qing ZHANG1Guan-lin XIE2Jun ZHU3Miao-miao LOU4Xue-ping ZHOU5Xiao-wei ZHANG6Guo-chang SUN7Bin LI8Bo ZHU9State 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; Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, P.R. China; JIN Gu-leiState 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. ChinaState 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. ChinaInstitute of Bioinformatics, Zhejiang University, Hangzhou 310029, P.R. ChinaState 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. ChinaState 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. ChinaCrop Management Station, Jiaxing 314051, P.R. ChinaState 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. ChinaState 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; Correspondence LI Bin, Tel: +86-571-88982412State 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; ZHU Bo, Tel: +86-571-88982412Horizontal 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 1547 genes while the pan-genome will increase up to 22624 genes when sequencing 1000 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.http://www.sciencedirect.com/science/article/pii/S2095311912600860Xanthomonascore and pan-genomegene gain/losshorizontal gene transfer |
| spellingShingle | Gu-lei JIN Guo-qing ZHANG Guan-lin XIE Jun ZHU Miao-miao LOU Xue-ping ZHOU Xiao-wei ZHANG Guo-chang SUN Bin LI Bo ZHU Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence Journal of Integrative Agriculture Xanthomonas core and pan-genome gene gain/loss horizontal gene transfer |
| title | Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence |
| title_full | Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence |
| title_fullStr | Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence |
| title_full_unstemmed | Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence |
| title_short | Evolution of Xanthomonas Gene Content: Gene Gain/Loss History and Species Divergence |
| title_sort | evolution of xanthomonas gene content gene gain loss history and species divergence |
| topic | Xanthomonas core and pan-genome gene gain/loss horizontal gene transfer |
| url | http://www.sciencedirect.com/science/article/pii/S2095311912600860 |
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