Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids

doi:10.1099/mgen.0.001004

	Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids
	Han, Kunming 1; Li, Yan1 ; Zhang, Zhenpeng 2; Sun, Liqin 1; Wang, En Tao 3; Li, Yan1
发表期刊	MICROBIAL GENOMICS
ISSN	2057-5858
	2023-05-01
卷号	9 期号:5 页码:12
关键词	conjugal transfer Rhizobium secretion system Sesbania cannabina symbiotic plasmid
DOI	10.1099/mgen.0.001004
通讯作者	Li, Yan(liyan0709@hotmail.com)
英文摘要	Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The suc-cessful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina- nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene back-ground of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local- condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD- independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
资助机构	Natural Science Foundation of Shandong Province
收录类别	SCI
语种	英语
关键词[WOS]	III SECRETION SYSTEM ; CONJUGATIVE TRANSFER ; SEQUENCE ; DIVERSITY ; GENE ; MOBILIZATION ; EVOLUTION ; EFFECTOR ; INSIGHTS ; IRBG74
研究领域[WOS]	Genetics & Heredity ; Microbiology
WOS记录号	WOS:000991100900005
引用统计
文献类型	期刊论文
条目标识符	http://ir.yic.ac.cn/handle/133337/32942
专题	海岸带生物学与生物资源利用重点实验室
通讯作者	Li, Yan
作者单位	1.Yantai Univ, Coll Life Sci, Yantai Key Lab Characterist Agr Bioresource Conser, Yantai 264005, Shandong, Peoples R China 2.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Bioresource Utilizat, Yantai, Peoples R China 3.Inst Politecn Nacl, Escuela Nacl Ciencias Biol, Dept Microbiol, Mexico City 11340, Mexico
推荐引用方式 GB/T 7714	Han, Kunming,Li, Yan,Zhang, Zhenpeng,et al. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids[J]. MICROBIAL GENOMICS,2023,9(5):12.
APA	Han, Kunming,Li, Yan,Zhang, Zhenpeng,Sun, Liqin,Wang, En Tao,&Li, Yan.(2023).Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids.MICROBIAL GENOMICS,9(5),12.
MLA	Han, Kunming,et al."Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids".MICROBIAL GENOMICS 9.5(2023):12.