高效固氮大豆根瘤菌SMH12的全基因组测序及比较基因组分析

Whole genome sequencing and genome comparative analysis using the highly nitrogen-fixing strain, Sinorhizobium fredii SMH12

费氏中华根瘤菌SMH12(Sinorhizobium fredii SMH12),生长代时较短,属于快生型大豆根瘤菌.SMH12具有高效固氮、宿主范围广、匹配性强、遗传物质稳定等特点,为充分开发该菌应用潜力和研究价值,有必要解析SMH12的基因组序列.采用Illumina Hiseq与Pacbio测序技术相结合对SMH12菌株进行全基因组测序.进一步使用相关软件对测序数据进行基因组的组装、基因预测与功能注释、COG/GO聚类分析以及比较基因组分析.测序结果显示,SMH12基因组包含1条染色体和2个质粒,染色体大小为4022924 bp,质粒pSfSMH12a大小为2394395 bp,质粒pSfSMH12b大小为556376bp,序列已提交至GenBank数据库,登录号为CP035038-CP035040.基因预测与rRNA、tRNA查找显示,SMH12基因组含有6836个基因,有9个rRNA和55个tRNA.比较基因组分析的直系同源基因比对与共线性分析显示,SMH12与S.fredii HH103大部分基因相同,亲缘关系最密切;只有约17%的基因不同.COG分类比较分析显示,SMH12中转座因子和碳水化合物的转运与代谢这两类相关基因的占比明显高于Bradyrhizobium diazoefficiens USAD110.本研究首次报道SMH12基因组序列并分析了其基因组基本特征,与其他代表性大豆根瘤菌进行了比较基因组分析.结果丰富了根瘤菌基因组数据库,也为构建高效固氮的大豆根瘤菌工程菌提供了一定依据和基因资源.(图6表2参35)

Sinorhizobium fredii SMH12 is a fast-growing soybean rhizobium that has a short generation time,high symbiotic nitrogen-fixing efficiency,wide host range,strong compatibility,and genetic stability.To fully utilize the potential application of SMH12 in agricultural production and scientific research,it is imperative that whole genome sequencing of S.fredii SMH12 be carried out followed by a comparative analysis with a related rhizobia genome.Whole-genome sequencing of SMH12 was carried out by Illumina Hiseq and Pacbio sequencing.Genome assembly,gene prediction and functional annotation,GO/COG cluster analysis,and comparative genomic analysis were carried out using the relevant bioinformatics software.The SMH12 genome was found to contain 1 chromosome and 2 plasmids possessing sizes of 4022924 bp,2394395 bp(plasmid pSfSMH12a),and 556376 bp(plasmid pSfSMH12b),respectively.The genomic sequences were deposited in GenBank with accession numbers CP035038-CP035040.The SMH12 genome was found to contain 6836 genes,including 9 rRNAs and 55 tRNAs.Comparative genomic analysis revealed that only 17%of genes differed between SMH12 and S.fredii HH103,which further suggest that SMH12 has the closest genetic relation with HH103.A classified comparative analysis based on the proteins COG category showed that the proportion of X(mobilome,prophages,transposons)and G(carbohydrate transport and metabolism)in SMH12 was significantly higher than that in Bradyrhizobium diazoefficiens USAD110.Altogether,genome sequencing and comparative analysis of S.fredii SMH12 provided novel gene resources that could be deposited into the database of rhizobia genomes.They also revealed the scientific basis and guidance required to construct an engineered rhizobia strain with high nitrogen-fixing ability.