摘要
通过对金乡大蒜根际土壤的分离、筛选,获得一株体内存在降解邻苯二酚等芳香族化合物及氧化砷、铜等代谢途径的菌株,经16S rDNA鉴定为非脱羧勒克氏菌,命名为YZ30,并进行了全基因组测序。该菌株利用二代Illumina Hiseq和三代PacBio相结合的的测序方式,运用SOAPdenovo软件进行数据组装,采用BLAST+、eggNOG、PromPredict、antiSMASH、IslandPath-DIMOB等软件进行基因预测、基因注释、启动子预测、次级代谢产物基因簇预测和基因组岛预测等。最终测得包括两个质粒基因组在内,总长度为4958825 bp,G+C含量平均为56.02%,预测到4725个基因、57个串联重复序列、85个tRNA、25个rRNA。在NR、Swiss-Prot、Pfam、COG、GO和KEGG数据库中,分别有4724,3984,4127,4285,3490和2976个基因能够提取到注释信息。同时,还预测到4个次级代谢产物基因簇。基因组测序数据提交至NCBI获得GenBank登录号:CP068234。此研究从基因组层面上解析了YZ30菌株降解或氧化金乡大蒜土壤中部分有毒物质的基本原理提供了数据支持,为深入了解、开发非脱羧勒克氏菌处理污染物质提供了思路,对非脱羧勒克氏菌的后续研究具有重大意义。
Through isolation and screening of garlic rhizosphere soil in Jinxiang,and a strain was obtained,which had the metabolism pathway of pyrocatechol and arsenic oxide and copper,it was identified as Leckercia adecarboxylata strain by 16 S rDNA,named YZ30,and sequenced the whole genome.The second-generation Illumina hiseq and the third-generation pacbio were used for sequencing,and the data were assembled by soapdenovo software.BLAST+,eggNOG,PromPredict,antiSMASH,IslandPath DIMOB software were used for gene prediction,gene annotation,promoter prediction,secondary metabolite gene cluster prediction and genome island prediction.The total length of the two plasmids was 4958825 bp,the content of G+C was 56.02%,4725 genes,57 tandem repeats,85 tRNAs and 25 rRNAs were predicted.In NR,Swiss Prot,Pfam,COG,GO and KEGG databases,4724,3984,4127,4285,3490 and 2976 genes can extract annotation information.At the same time,four gene clusters of secondary metabolites were predicted.The sequencing data from this article are available in the GenBank database(accession number CP068234).This study analyzed the basic principle of YZ30 strain degradation or oxidation of some toxic substances in garlic soil in Jinxiang from the genomic level,provided data support,provided ideas for further understanding and development of L.adecarboxylata to treat pollutants,and had great significance for the subsequent research of L.adecarboxylata.
作者
吴生亮
叶子兰
张彤彤
赵莉
阮期平
WU Sheng-liang;YE Zi-lan;ZHANG Tong-tong;ZHAO Li;RUAN Qi-ping(College of Resources and Environmental Engineering,Mian Yang Teachers College,Mianyang 621000,China;Key Laboratories for Molecular Biology and Biopharmaceuticals,Mian Yang Teachers College,Mianyang 621000,China;College of Life Science and Technology,Mian Yang Teachers College,Mianyang 621000,China)
出处
《药物生物技术》
CAS
2022年第1期8-15,共8页
Pharmaceutical Biotechnology
基金
四川省科技厅重点项目(No.2016JY0038)。
