耐草甘膦菌株Pantoea rodasii S1536全基因组测序及比较基因组分析

Whole-Genome Sequencing and Comparative Genome Analysis of Glyphosate-Resistant Strain Pantoea rodasii S1536

耐草甘膦菌株泛菌属S1536(Pantoea rodasii S1536)是从草甘膦污染土壤中分离筛选出来的一种革兰氏阴性菌,对草甘膦的抗性能高达400 mmol/L。本研究首次通过PacBio RSII平台对泛菌属S1536进行全基因组测序,使用SMRT portal软件对reads进行组装,获得10个contigs,最终获得高质量且无间隔的泛菌属S1536基因组包含1条染色体和2个质粒,序列全长为5.16 Mb,其GC含量为55.16%。本研究进一步对基因组序列进行基因预测与功能注释、COG和GO聚类分析,预测了次级代谢产物合成基因簇及草甘膦抗性机制,最终得到编码基因有4843个,4656个蛋白获得COG功能注释,预测到2个NRPS类基因簇、1个thiopeptide类基因簇和1个hserlactone-arylpolyene类基因簇。莽草酸代谢途径关键酶EPSP合酶基因分析表明,泛菌属S1536中的EPSP合酶属于ClassⅠ型EPSPS。根据已报道的3株同一种Pantoea rodasii strain ND03、Pantoea rodasii strain DSM 26611和Pantoea rodasii strain LMG 26273的基因组信息进行全基因组关联比较分析,结果显示4株菌虽然属于同一种,但在进化中产生了较大差异。相关研究结果将为泛菌属S1536功能基因组学研究、耐除草剂机制的研究及耐除草剂基因的挖掘提供基础数据。

Glyphosate resistant strain S1536(Pantoea rodasii S1536)is a gram-negative bacterium isolated from glyphosate contaminated soil.Its resistance to glyphosate is as high as 400 mmol/L.In this study,the whole-genome sequencing of S1536 was the first sequenced through PacBio RSII platform.Reads were assembled using SMRT portal software,and 10 contigs were obtained.The whole genome sequences of S1536 with high-quality and 0-gap was composed of 1 chromosome and 2 plasmids.Its size was about 5.16 Mb with GC content of 55.16%.Then,gene prediction and functional annotation,COG and GO cluster analysis and prediction of secondary metabolite synthesis gene cluster and analysis of resistance mechanism of glyphosate were further carried out for genome sequences,and 4843 coding genes and 4656 proteins were obtained with functional annotation of COG.Two NRPS gene clusters,one thiopeptide gene cluster and one hserlactone-arylpolyene gene cluster were predicted.The result of analysis key enzyme of shikimic acid metabolism pathway showed that EPSP synthase of S1536 belonged to ClassⅠEPSPS.The whole-genome comparative association analysis was performed based on the reported genomic information on the same species of strain ND03,strain DSM 26611 and strain LMG 26273,the results showed that although the four strains belonged to the same species,great differences were generated in evolution.The relevant results will provide basic data for further study of functional genomics,herbicide tolerance mechanism and herbicide tolerance genes.