新根瘤菌属(Neorhizobium)隶属于根瘤菌科(Rhizobiaceae),目前有效发布了 8个种.为了探究该属下不同模式菌株的全基因组分子机理和遗传特征,本文采用Prodigal等软件对这 8个模式菌株的全基因组序列进行基因预测、功能注释和系统发育分析,并在此基础上进行了基因组比较分析.基因组预测结果显示,这 8个模式菌株的CDS(Coding Sequences)数量为 4 471～6 669个,GC含量在 60.0%至 61.6%之间,rRNA数量为 3至 9个,tRNA数量为 43至 51个.通过比较基因组分析发现,所有菌株共享的直系同源基因簇有 2 563个,独立拥有的基因簇数量少.通过平均核苷酸一致性(ANI)、数字DNA-DNA杂交(dDDH)和系统发育树的分析,发现菌株CCBAU 05176T和菌株T17_20T具有最高的同源性,而菌株T786T和NTR19T的遗传距离最远.COG(Cluster of Orthologous Groups of Proteins)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类的比较分析显示,注释的基因功能整体差异较小,但在SL-1T中,异种生物的生物降解和代谢的注释比例和数量明显高于其他模式菌株.本研究为新根瘤菌属的系统分类以及在生态系统中的应用奠定了理论基础.
Comparative analysis on whole genome sequences of type strains in the genus of Neorhizobium
The genus Neorhizobium belongs to the family Rhizobiaceae,and there are only eight validly published species within this genus.To investigate the molecular mechanisms and genetic characteristics of these eight strains,we used Prodigal and other software to predict and annotate genes,perform phylogenetic analysis based on whole genome sequences,and compare and analyze the genomes.The predictions showed that the CDS(Coding Sequences),GC content,rRNA,and tRNA ranges are 4 471-6 669,60.0%-61.6%,3-9,and 43-51,respectively.Comparative analysis of the genomes identified 2 563 orthologous gene clusters that are shared among all strains while only few specific gene clusters are independently inherent.By using average nucleotide identity(ANI),digital DNA-DNA hybridization(dDDH),and phylogenetic tree,we found that CCBAU 05176T and T17_20T exhibit the highest homology,while T786T and NTR19T show the greatest genetic distance.Based on comparative analysis of COG(Cluster of Orthologous Groups of Proteins)and KEGG(Kyoto Encyclopedia of Genes and Genomes)classifications,we found that the annotated gene functions are generally consistent,but the number and proportion of xenobiotic biodegradation and metabolism genes are significantly higher in strain SL-1T than in other strains.Taken together,our findings help to lay a foundation for the future systematic taxonomy and application of the Neorhizobium genus in different ecosystems.
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