State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P, R, China.
BMC Genomics. 2014 Jun 6;15(1):440. doi: 10.1186/1471-2164-15-440.
Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general.
In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species.
Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome.
迫切需要基于基因组序列的证据来确认 MAFF303099 菌株与 M. huakuii 之间的系统发育关系。为了确定 M. huakuii 菌株 7653R 和 MAFF303099 之间宿主特异性差异的潜在原因，还需要在基因组水平上比较几个可能的决定因素。深入了解可整合到 Mesorhizobium 主染色体中形成基因组岛的移动遗传元件，将丰富我们对基因组动态如何促进 Mesorhizobium 进化的认识。
在这项研究中，我们对 7653R 的全基因组进行了测序，并与其他五个 Mesorhizobium 基因组进行了比较。发现 7653R 和 MAFF303099 的基因组共享一大组直系同源物，最重要的是，保守的染色体骨架和更大的完全保守的同线性块。我们还确定了导致这两个菌株宿主特异性不同的候选分子差异。最后，我们重建了一个祖先 Mesorhizobium 基因组岛，它在不同的 Mesorhizobium 物种中已经进化成多种形式。
我们的直系同源物和同线性分析牢固地确立了 MAFF303099 是 M. huakuii 的一个菌株。结瘤因子和分泌系统 T3SS、T4SS 和 T6SS 的差异可能是 7653R 和 MAFF303099 菌株独特宿主特异性的原因。7653R 的质粒可能是通过从 7653R 染色体上切除原始基因组岛而产生的。
