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[1]成家龙 陈大松 李友国**.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*[J].应用与环境生物学报,2020,26(01):1-13.[doi:10.19675/j.cnki.1006-687x.2019.04011]
 CHENG Jialong,CHEN Dasong & LI Youguo**.Whole genome sequencing of highly nitrogen-fixing strain Sinorhizobium fredii SMH12 and genome comparative analysis *[J].Chinese Journal of Applied & Environmental Biology,2020,26(01):1-13.[doi:10.19675/j.cnki.1006-687x.2019.04011]
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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*()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
26卷
期数:
2020年01期
页码:
1-13
栏目:
研究论文
出版日期:
2020-01-25

文章信息/Info

Title:
Whole genome sequencing of highly nitrogen-fixing strain Sinorhizobium fredii SMH12 and genome comparative analysis *
作者:
成家龙 陈大松 李友国**
华中农业大学生命科学技术学院,农业微生物学国家重点实验室 武汉 430070
Author(s):
CHENG Jialong CHEN Dasong & LI Youguo**
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
关键词:
高效固氮费氏中华根瘤菌SMH12全基因组测序比较基因组分析
Keywords:
high-efficiency nitrogen-fixing Sinorhizobium fredii SMH12 whole genome sequencing comparative genomic analysis
DOI:
10.19675/j.cnki.1006-687x.2019.04011
摘要:
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4 022 924 bp,质粒pSfSMH12a大小为2 394 395 bp,质粒pSfSMH12b大小为556 376bp,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6 836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。
Abstract:
Sinorhizobium fredii SMH12 is a fast-growing soybean rhizobium. It has a short generation time, high symbiotic nitrogen-fixing efficiency, wide host range, strong compatibility and genetic stability. In order to make full use of its potential application in agricultural production and scientific research,it is necessary to conduct a whole genome sequencing of S. fredii SMH12 and perform a comparative analysis with 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 had been done by relevant bioinformatics software. SMH12 genome contains 1 chromosome and 2 plasmids, which are in the size of 4 022 924 bp, 2 394 395 bp (plasmid pSfSMH12a) and 556 376 bp (plasmid pSfSMH12b) respectively. The genomic sequence has been deposited in the GenBank with the accession numbers CP035038 to CP035040. There are 6 836 genes within the SMH12 genome, including 9 rRNAs and 55 tRNAs. Comparative genomic analysis showed there are only 17% different genes found between SMH12 and S. fredii HH103, suggesting SMH12 has the closest genetic relation with HH103. A classified comparative analysis in terms of the proteins COG category showed that the proportion of X (mobilome, prophages, transposons) and G (carbohydrate transport and metabolism) in SMH12 is significantly higher than that of Bradyrhizobium diazoefficiens USAD110. The genome sequencing and comparative analysis of S. fredii SMH12 has provided novel gene resources into the database of rhizobia genomes, and it also provided scientific basis and guidance for the construction of engineered rhizobia strain with highly nitrogen-fixing ability.

相似文献/References:

[1]张武,田润,申佩弘,等.费氏中华根瘤菌15142的cysDN基因克隆及其相关功能[J].应用与环境生物学报,2011,17(06):864.[doi:10.3724/SP.J.1145.2011.00864]
 ZHANG Wu,TIAN Run,SHEN Peihong,et al.Cloning and Related Function of cysDN in Sinorhizobium fredii 15142[J].Chinese Journal of Applied & Environmental Biology,2011,17(01):864.[doi:10.3724/SP.J.1145.2011.00864]
[2]宋张杨,马婷婷,周燕,等.不同根瘤菌中突变cysDN基因对硫酸盐同化途径的影响[J].应用与环境生物学报,2015,21(02):242.[doi:10.3724/SP.J.1145.2014.10020]
 SONG Zhangyang,MA Tingting,ZHOU Yan,et al.Effect of cysDN genes in different rhziobium on the sulfate assimilation pathway[J].Chinese Journal of Applied & Environmental Biology,2015,21(01):242.[doi:10.3724/SP.J.1145.2014.10020]

备注/Memo

备注/Memo:
收稿日期 Received: 2019-04-05 接受日期 Accepted: 2019-05-13
*国家重点计划研发项目(2018YFD0201006)和国家自然科学基金项目(31670243)资助
**通讯作者 Corresponding authors (E-mail: youguoli@mail.hzau.edu.cn)
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更新日期/Last Update: 2019-05-15