Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

Tian, Chang Fu, Zhou, Yuan Jie, Zhang, Yan Ming, Li, Qin Qin, Zhang, Yun Zeng, Li, Dong Fang, Wang, Shuang, Wang, Jun, Gilbert, Luz B., Li, Ying Rui and Chen, Wen Xin (2012) Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proceedings of the National Academy of Sciences of the United States of America, 109 22: 8629-8634. doi:10.1073/pnas.1120436109


Author Tian, Chang Fu
Zhou, Yuan Jie
Zhang, Yan Ming
Li, Qin Qin
Zhang, Yun Zeng
Li, Dong Fang
Wang, Shuang
Wang, Jun
Gilbert, Luz B.
Li, Ying Rui
Chen, Wen Xin
Title Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
Journal name Proceedings of the National Academy of Sciences of the United States of America   Check publisher's open access policy
ISSN 0027-8424
1091-6490
Publication date 2012-05-29
Sub-type Article (original research)
DOI 10.1073/pnas.1120436109
Open Access Status Not yet assessed
Volume 109
Issue 22
Start page 8629
End page 8634
Total pages 6
Place of publication Washington, DC United States
Publisher National Academy of Sciences
Language eng
Formatted abstract
The rhizobium–legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium–legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.
Keyword Glycine
Prokaryote
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Fri, 04 Sep 2015, 01:20:10 EST by Mr Mathew Carter on behalf of Institute for Molecular Bioscience