Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

Abstract

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct “tumorigenes” clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high‐quality, closed genomes of representatives of the “tumorigenes” clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the “tumorigenes” clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the “tumorigenes” clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids

“…In this study, a comprehensive comparative sequence analysis of Ti plasmids occurring in members of the clade “tumorigenes” of the family Rhizobiaceae (“tumorigenes” Ti plasmids) was performed. This not only primarily included plasmids pTi932, pTi1078, and pTi6.2 sequenced in our recent work ( Kuzmanović et al 2023 ) and reannotated in this study but also closely related plasmids associated with “tumorigenes” strains isolated in the United States (pTiK1/93, pTiK15/93, pTiB21/90, pTiL51/94, and pTiB230/85; table 1 ). These plasmids vary in size (∼197–455 kb) and all belong to the repABC plasmid family, which is typical for Ti/Ri plasmids ( Farrand 1998 ; Pinto et al 2012 ).…”

“…Agrobacteria contain multipartite genomes, consisting of a main chromosome, chromid(s), and (mega)plasmid(s) ( Harrison et al 2010 ; Slater et al 2013 ; Kuzmanović et al 2023 ). Particularly important are oncogenic plasmids that are indispensable for the pathogenicity of agrobacteria.…”

“…These data will contribute to a better understanding of evolution and ecology of these replicons. In our recent work, we characterized the novel “tumorigenes” clade of the family Rhizobiaceae , which includes tumorigenic bacteria Rhizobium tumorigenes and Rhizobium rhododendri isolated from crown gall tumors of blackberry and rhododendron, respectively ( Kuzmanović et al 2018 ; Kuzmanović et al 2019 ; Kuzmanović et al 2023 ). Analysis of draft genome sequences of the rhododendron strains suggested that they carry atypical Ti plasmids ( Kuzmanović et al 2019 ).…”

“…Analysis of draft genome sequences of the rhododendron strains suggested that they carry atypical Ti plasmids ( Kuzmanović et al 2019 ). We subsequently generated complete genome sequences of representative strains of R. tumorigenes (932 and 1078 T ) and R. rhododendri (rho-6.2 T ) ( Kuzmanović et al 2023 ). Here, we analyzed the sequences of plasmids pTi932, pTi1078, and pTi6.2, as well as related Ti plasmids of R. rhododendri strains originating from the United States.…”

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria: Minutes of the closed annual meeting, videoconference on 2 October 2023, followed by online discussion until 31 December 2023

“…11.2 Kuzmanović mentioned a new publication in the taxonomy of agrobacteria [6], which described the new species Rhizobium rhododendri within the distinct ‘tumorigenes’ clade of the genus Rhizobium .…”