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

IF 3.9 3区生物学 Q2 MICROBIOLOGY

MicrobiologyOpen Pub Date : 2023-03-31 DOI:10.1002/mbo3.1352

Nemanja Kuzmanović, George C. diCenzo, Boyke Bunk, Cathrin Spröer, Anja Frühling, Meina Neumann-Schaal, Jörg Overmann, Kornelia Smalla

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引用次数: 3

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.

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根瘤菌科“致瘤性”分支的基因组学研究及杜鹃花根瘤菌的描述。

根瘤菌科的致瘤性成员，被称为农杆菌，是世界各地各种作物的冠和甘蔗瘿病的罪魁祸首。致瘤性农杆菌常见于农杆菌属、异氮根瘤菌属和根瘤菌属。在这项研究中，我们分析了根瘤菌属的一个独特的“致瘤”分支，其中包括致瘤物种根瘤菌，以及引起杜鹃花冠瘿病的菌株。在这里，高质量的、封闭的“致瘤”进化支代表基因组被生成，随后进行比较基因组和系统基因组分析。此外，还分析了“致瘤性”分支的代表表型特征。结果表明，从杜鹃花中分离出的致瘤菌株是根瘤菌属的一个新种，命名为rhododendri sp. 11。该物种还包括来自美国蓝莓和喜马拉雅黑莓的其他菌株，其基因组序列从GenBank中检索。瘤源性红发菌和杜鹃属红发菌都含有多部基因组，包括染色体、推定的染色粒和巨质粒。同源性和系统发育分析表明，杜鹃花的一个大的推定染色质是由一个祖先的大质粒和两个推定的染色质协整而成的。此外，还鉴定了这两种“致瘤性”枝的特异性基因簇，并对其生物学功能和在杜鹃花和致瘤性杜鹃花生态多样性中的作用进行了预测和讨论。

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来源期刊

MicrobiologyOpen MICROBIOLOGY-

CiteScore

8.00

自引率

0.00%

发文量

审稿时长

20 weeks

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