Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris

Tong, Wenjun; Li, Xiangchen; Huo, Yunyun; Zhang, Lu; Cao, Ying; Wang, En Tao; Chen, Weimin; Tao, Shiheng; Wei, Gehong

doi:10.1016/j.syapm.2018.03.001

Cited by 31 publications

(31 citation statements)

References 85 publications

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“…Our inferred species tree of BCC reconstructed by these markers provided us with an accurate phylogenetic relationship. Together with dDDH and ANI, two methods that are useful for species demarcation and are powerful in BCC species differentiation [1,64,65], we delineated BCC species as 36 clusters. The results showed that the 22 currently known species correspond to 22 of these clusters (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Yuan¹,

Zhou²,

Zhou³

et al. 2020

Biol Direct

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Background: Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods: We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results: We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions: This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer: This article was reviewed by Dr. Xianwen Ren.

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Section: Discussionmentioning

confidence: 99%

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Yuan¹,

Zhou²,

Zhou³

et al. 2020

Biol Direct

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“…Inicialmente, la diversidad de R. etli se estudió con patrones electroforéticos de enzimas metabólicas y la alta diversidad encontrada se atribuyó a su antigüedad, además se discutió que R. etli podría abarcar a distintas especies (Piñero et al, 1988). Posteriormente, se ha identificado una diversidad amplia de linajes de rizobios de los nódulos de Phaseolus vulgaris con análisis tanto moleculares (Miranda-Sánchez et al, 2016;Ribeiro et al 2013;Wang et al, 2011) como genómicos en distintas regiones de México, del Caribe (Carrascal et al, 2016;Díaz-Alcántara et al, 2014;Santamaría et al, 2017;Tong et al, 2018) y de China, donde el frijol fue introducido y es cultivado a gran escala (Cao et al, 2014). Se han reclasificado a algunas cepas previamente consideradas como R. etli en otras especies cercanas, R. phaseoli (Ramírez-Bahena et al, 2008), R. ecuadorense (Ribeiro et al, 2015) y R. esperanzae (Cordeiro et al, 2017), mientras otros linajes nuevos no han sido todavía nombrados como nuevas especies (López-Guerrero et al, 2012).…”

Section: Rizobios Encontrados En Méxicounclassified

La diversidad de rizobios nativos de México a la luz de la genómica

et al. 2019

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chiapanecum y S. americanum, además de nuevos linajes de rizobios. El análisis basado en datos genómicos muestra que las especies de Rhizobium cercanas genéticamente comparten significativamente el genoma cromosomal y difieren más en genes contenidos en plásmidos, excepto en algunos plásmidos simbióticos que pueden encontrarse conservados aún en especies no relacionadas que contienen el mismo simbiovar. Los avances en la genómica de rizobios han permitido proponer nuevas especies usando comparaciones genómicas globales y contribuirán al uso más adecuado de estas bacterias como biofertilizantes.

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“…Approximately 89% of these isolates were Rhizobium, including six defined species and eight novel genospecies, while the remaining strains were Bradyrhizobium (2.4%) and Ensifer (8.4%) [13]. To date, several species such as R. anhuiense [15], E. fredii [14], and some genospecies from Bradyrhizobium [13] and Ensifer [14] have only been found in China. Some of these common bean-nodulating rhizobia were also found in association with other hosts, such as Vicia faba (fava bean) and Trifolium spp.…”

Section: Introductionmentioning

confidence: 99%

“…Some of these common bean-nodulating rhizobia were also found in association with other hosts, such as Vicia faba (fava bean) and Trifolium spp. (clover) in China [15]. How such an extraordinary variety of genotypes from three distinct genera (Rhizobium, Bradyrhizobium, and Ensifer) evolved into microsymbionts of common bean after its introduction into China is very interesting.…”

Section: Introductionmentioning

confidence: 99%

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

Tong

Wang

et al. 2020

BMC Genomics

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Background: Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts. Results: Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions. Conclusions: The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.

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Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris

Cited by 31 publications

References 85 publications

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

La diversidad de rizobios nativos de México a la luz de la genómica

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

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