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Microbial Genomics logo Microbial Genomics

Volume 9, Issue 5

Comparative genome analysis of -nodulating spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids Open Access

Abstract

Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the and 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, -nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of 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 strains associated with , 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 , the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345–402 kb containing complete , , , 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 species. These results indicate that stringently selects a certain symbiosis gene background 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 , indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a -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.

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  • Accepted:
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Keyword(s): conjugal transfer , Rhizobium , secretion system , Sesbania cannabina and symbiotic plasmid
Funding
This study was supported by the:
  • Natural Science Foundation of Shandong Province (Award ZR2020MC043)
    • Principle Award Recipient: LiqinSun
  • Natural Science Foundation of Shandong Province (Award ZR202102280248)
    • Principle Award Recipient: YanLi
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-05-03
2025-06-24
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/content/journal/mgen/10.1099/mgen.0.001004
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Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids
M Gen 9, 001004 (2023); https://doi.org/10.1099/mgen.0.001004
/content/journal/mgen/10.1099/mgen.0.001004
/content/journal/mgen/10.1099/mgen.0.001004
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