Comparative analysis of rhizobial chromosomes and plasmids to estimate their evolutionary relationships

Li, Dongying; Luo, Yane; Zhao, Liang; Liu, Zhenshan; Chou, Ming-Yi; Wang, Entao

doi:10.1016/j.plasmid.2018.03.001

Cited by 8 publications

(8 citation statements)

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“…Despite many effort to define Rhizobium species with polyphasic taxonomy and genomic and phylogenomic approaches, the question concerning the biological meaning of genomic clusters within species and whether or not they are equivalent to species remains (Tong et al, 2018; Wang et al, 2018). We address this outstanding question, by carrying out a detailed genomic and phylogenomic comparison of recently released genomes of common-bean nodulating Rhizobium and a selected set of Rhizobium reference genomes available in GenBank.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters

et al. 2019

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The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium , but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium . The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters

et al. 2019

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“…Members of the family Rhizobiaceae exhibit signs of replicon co-evolution (Slater et al 534 2009; Lassalle et al 2017;Wang et al 2018) and cross-replicon interactions (Ronson et 535 al. 1987;Heidelberg et al 2000;Barnett et al 2004;Bobik et al 2006;Galardini et al 536 2015; Pini et al 2015;Ramachandran et al 2017;diCenzo et al 2018), despite 537 remarkable strain-to-strain variation and the prevalence of large-scale rearrangements 538 in secondary replicons (Orozco-Mosqueda Mdel et al 2009;Mazur et al 2011;Lopez-the Ti plasmid of a different octopine-type strain of A. tumefaciens (Machida et al 1984) 562 and is part of a larger family of IS-elements found within a variety of bacteria (Han et al 563 2001; Gourbeyre et al 2010).…”

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confidence: 99%

Destabilization of the Tumor-Inducing Plasmid from an Octopine-TypeAgrobacterium tumefaciensLineage Drives a Large Deletion in the Co-Resident At Megaplasmid

Barton

Platt

Rusch

et al. 2019

Preprint

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1Bacteria with multi-replicon genome organizations, including members of the family 2 Rhizobiaceae, often carry a variety of niche-associated functions on large plasmids. 3 While evidence exists for cross-replicon interactions and co-evolution between replicons 4 in many of these systems, remarkable strain-to-strain variation is also observed for 5 extrachromosomal elements, suggesting increased genetic plasticity. Here, we show 6 that curing of the tumor-inducing virulence plasmid (pTi) of an octopine-type 7 Agrobacterium tumefaciens lineage leads to a large deletion in the co-resident At 8 megaplasmid (pAt). The deletion event is mediated by a repetitive IS-element, IS66, 9 and results in a variety of environment-dependent fitness consequences, including loss 10 of independent conjugal transfer of the plasmid. Interestingly, a related and otherwise 11 wild-type A. tumefaciens strain is missing exactly the same large pAt segment as the 12 pAt deletion derivatives, suggesting a similar event over its natural history. Overall, the 13 findings presented here uncover a novel genetic interaction between the two large 14 plasmids of A. tumefaciens and provide evidence for cross-replicon integration and co-15 evolution of these plasmids. 16 Bacteria exhibit a diversity of genomic architectures and contain replicons that range 18 from small, transient plasmids and megaplasmids, to chromids, to secondary and 19 primary chromosomes (diCenzo and Finan 2017). Primary chromosomes are the largest 20 replicons encoding core functions, whereas any replicating elements in addition to the 21 primary chromosome are defined as secondary replicons. Secondary chromosomes are 48 limitation to the coexistence of multiple replicons and have been observed in diverse 49 bacterial species, including species of Vibrio (Heidelberg et al. 2000; Ramachandran et 50 al. 2017) and Sinorhizobium (Ronson et al. 1987; Barnett et al. 2004; Bobik et al. 2006; 51 Galardini et al. 2015; Pini et al. 2015; diCenzo et al. 2018). In most cases, chromosomal 52 factors influence the regulation of secondary replicon factors, with limited regulation in 53 the opposite direction (Ronson et al. 1987; Barnett et al. 2004; Bobik et al. 2006; Agnoli 54 et al. 2012; Galardini et al. 2015; Pini et al. 2015; diCenzo et al. 2018), likely due to 55 intolerance of integral pathway perturbation and the suppression of costly accessory 56 functions required to stabilize secondary replicons. However, metabolic redundancy has 57 been observed between rhizobial replicons (González et al. 2005; diCenzo and Finan 58 2017), suggesting that favorable interaction and pathway integration between primary 59 and secondary replicons can occur. However, because the majority of organisms 60 possessing multi-partite genomes exist and transition between multiple environmental 61 reservoirs, and are often host-associated, the extent to which cross-replicon interactions 62 occur and their consequences are often not determined.63Here, we characterize a cross-replicon genetic interaction in ...

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“…Таким образом, выявлены достоверные различия по встречаемости ГО, относящихся к акцессорным элементам корового генома, у природных штаммов S. meliloti с разными хромосомными типами. Полученные результаты согласуются с данными для других видов клубеньковых бактерий и энтеробактерий [9,26] и свидетельствуют в пользу того, что определенные акцессорные элементы могут быть ассоциированы с определенными сочетаниями коровых последовательностей.…”

Section: таблица 1 неравновесие по сцеплению (Ld) между маркерами M-iunclassified

“…Оценка неравновесия по сцеплению (LD) маркерных последовательностей показала, что между метаболическими маркерами отсутствует или имеется низкий уровень генетической рекомбинации, на основании чего и согласно работе [10] они были использованы для определения сочетаний маркеров у 218 природных штаммов S. meliloti, сгруппированных далее в четыре хромосомных типа, различавшихся по наличию референс-и дивергентных последовательностей. Обнаружено, что географически изолированные популяции S. meliloti достоверно различались по встречаемости хромосомных типов, что согласуется с данными, полу-ченными для других видов ризобий [9,11,53]. В популяции каждого из рассмотренных генцентров (СКГ и ПАГ) выявлены штаммы с измененными метаболическими маркерами (хромосомный тип АII), доля которых среди К-изолятов была почти в 2 раза выше, чем среди П-изолятов, в обоих генцентрах.…”

Section: заключениеunclassified

“…core) [1][2][3][4][5][6][7]. Ортологи этих генов присутствуют, как правило, у всех штаммов одного вида/рода, а также у соответствующих им предполагаемых общих предков [8,9]. Изучение структуры генов у генетически неродственных штаммов бактерий на рестрикционном (полиморфизм длин рестрикционных фрагментов -ПДРФ) и/или нуклеотидном уровнях позволяет выявлять аллели с разным уровнем сходства, на основании которого штаммы объединяют в группы/кластеры [4,[9][10][11].…”

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Sinorhizobium meliloti: chromosomal types and genomic islands

Cherkasova

Евгеньевна²,

Muntyan

et al. 2019

Ecological genetics

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Background. Polymorphism analysis was done for the core genome sequences of nodule bacteria of S. meliloti species in order to identify chromosomal types and to evaluate the occurrence of accessory elements (genomic islands) in them. Materials and methods. Chromosomal studied loci were: betBC (marker M-I) and SMc04407-SMc04881 (marker M-II) both are related to metabolic processes and stress tolerance, and 16S-23S intergenic sequences (marker M-III) to search phylogenetical distance at intraspecies level. Results. Significant differences between the occurrence of alleles of gene-markers M-I/M-II and MIII were determined between strains related to tested the 5 typical groups and 9 subgroups of strains differing by geographical region/source (nodule, soil) of isolation, as well as by salt tolerance. Four chromosomal types were identified among tested S. meliloti native isolates and a preference occurence of one of the three islands Rm1021 in links with particular chromosomal type was shown. The significant prevalence of strains with particular chromosomal type was shown for S. meliloti populations native to centers of alfalfa diversity at the NE of Caucasus, as well as at NE of Kazakhstan (Aral sea related region), as well as in agrocenoses. Conclusion. It was predicted that strains inherited altered markers M-I/M-II may belong to divergent clonal lines occured in both centers of alfalfa diversity, while strains with altered sequences of all three markers could be a representatives of a new S. meliloti biovar(s), the formation of which is occurred much more intensively at the modern center of the introgressive hybridization of alfalfa at NE of Kazakhstan.

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Comparative analysis of rhizobial chromosomes and plasmids to estimate their evolutionary relationships

Cited by 8 publications

References 75 publications

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters

Destabilization of the Tumor-Inducing Plasmid from an Octopine-TypeAgrobacterium tumefaciensLineage Drives a Large Deletion in the Co-Resident At Megaplasmid

Sinorhizobium meliloti: chromosomal types and genomic islands

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