Draft genome sequence of type strain HBR26(T) and description of Rhizobium aethiopicum sp nov.

作者：Aserse Aregu Amsalu; Woyke Tanja; Kyrpides Nikos C; Whitman William B; Lindstrom Kristina

来源：Standards in Genomic Sciences, 2017, 12(1): 14.

DOI：10.1186/s40793-017-0220-z

<jats:title>Abstract</jats:title><jats:p><jats:italic>Rhizobium aethiopicum</jats:italic> sp. nov. is a newly proposed species within the genus <jats:italic>Rhizobium</jats:italic>. This species includes six rhizobial strains; which were isolated from root nodules of the legume plant <jats:italic>Phaseolus vulgaris</jats:italic> growing in soils of Ethiopia. The species fixes nitrogen effectively in symbiosis with the host plant <jats:italic>P. vulgaris,</jats:italic> and is composed of aerobic, Gram-negative staining, rod-shaped bacteria. The genome of type strain HBR26<jats:sup>T</jats:sup> of <jats:italic>R. aethiopicum</jats:italic> sp. nov. was one of the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic Encyclopedia project designed for soil and plant-associated and newly described type strains. The genome sequence is arranged in 62 scaffolds and consists of 6,557,588 bp length, with a 61% G + C content and 6221 protein-coding and 86 RNAs genes. The genome of HBR26<jats:sup>T</jats:sup> contains <jats:italic>repABC</jats:italic> genes (plasmid replication genes) homologous to the genes found in five different <jats:italic>Rhizobium etli</jats:italic> CFN42<jats:sup>T</jats:sup> plasmids, suggesting that HBR26<jats:sup>T</jats:sup> may have five additional replicons other than the chromosome. In the genome of HBR26<jats:sup>T</jats:sup>, the nodulation genes <jats:italic>nodB, nodC, nodS, nodI, nodJ</jats:italic> and <jats:italic>nodD</jats:italic> are located in the same module, and organized in a similar way as <jats:italic>nod</jats:italic> genes found in the genome of other known common bean-nodulating rhizobial species. <jats:italic>nodA</jats:italic> gene is found in a different scaffold, but it is also very similar to <jats:italic>nodA</jats:italic> genes of other bean-nodulating rhizobial strains. Though HBR26<jats:sup>T</jats:sup> is distinct on the phylogenetic tree and based on ANI analysis (the highest value 90.2% ANI with CFN42<jats:sup>T</jats:sup>) from other bean-nodulating species, these <jats:italic>nod</jats:italic> genes and most nitrogen-fixing genes found in the genome of HBR26<jats:sup>T</jats:sup> share high identity with the corresponding genes of known bean-nodulating rhizobial species (96–100% identity). This suggests that symbiotic genes might be shared between bean-nodulating rhizobia through horizontal gene transfer. <jats:italic>R. aethiopicum</jats:italic> sp. nov. was grouped into the genus <jats:italic>Rhizobium</jats:italic> but was distinct from all recognized species of that genus by phylogenetic analyses of combined sequences of the housekeeping genes <jats:italic>recA</jats:italic> and <jats:italic>glnII</jats:italic>. The closest reference type strains for HBR26<jats:sup>T</jats:sup> were <jats:italic>R. etli</jats:italic> CFN42<jats:sup>T</jats:sup> (94% similarity of the combined <jats:italic>recA</jats:italic> and <jats:italic>glnII</jats:italic> sequences) and <jats:italic>Rhizobium bangladeshense</jats:italic> BLR175<jats:sup>T</jats:sup> (93%). Genomic ANI calculation based on protein-coding genes also revealed that the closest reference strains were <jats:italic>R. bangladeshense</jats:italic> BLR175<jats:sup>T</jats:sup> and <jats:italic>R. etli</jats:italic> CFN42<jats:sup>T</jats:sup> with ANI values 91.8 and 90.2%, respectively. Nevertheless, the ANI values between HBR26<jats:sup>T</jats:sup> and BLR175<jats:sup>T</jats:sup> or CFN42<jats:sup>T</jats:sup> are far lower than the cutoff value of ANI (&gt; = 96%) between strains in the same species, confirming that HBR26<jats:sup>T</jats:sup> belongs to a novel species. Thus, on the basis of phylogenetic, comparative genomic analyses and ANI results, we formally propose the creation of <jats:italic>R. aethiopicum</jats:italic> sp. nov. with strain HBR26<jats:sup>T</jats:sup> (=HAMBI 3550<jats:sup>T</jats:sup>=LMG 29711<jats:sup>T</jats:sup>) as the type strain. The genome assembly and annotation data is deposited in the DOE JGI portal and also available at European Nucleotide Archive under accession numbers FMAJ01000001-FMAJ01000062.</jats:p>

• 出版日期2017-1-26