Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis
Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis
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副地衣芽孢杆菌 MDJK30 及其密切相关物种的比较基因组分析揭示了副地衣芽孢杆菌和地衣芽孢杆菌之间的进化关系
DOI：
10.1186/s12864-019-5646-9
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发表时间：
2019-04-11
期刊：
影响因子：
4.4
通讯作者：
Wang, Chengqiang
中科院分区：
文献类型：
--
作者：
Du, Yuhui;Ma, Jinjin;Wang, Chengqiang
芽孢杆菌属的成员是重要的植物生长促进根瘤菌，作为生物防治剂。副苔藓芽孢杆菌mdjk30是从牡丹根际分离得到的一种抑制植物病原菌和真菌的PGPR。为了进一步揭示MDJK30及其近缘品系促进植物生长性状的遗传机制，我们利用比较基因组学方法对MDJK30及其近缘品系的遗传多样性和进化关系进行了研究。paralicheniformisandB。地衣芽。结果基于b的比较基因组学分析。对副衣原体mdjk30和其他55种先前报道的芽孢杆菌菌株进行检测。MDJK30的进化位置及与b。paralicheniformisandB。通过研究地衣虫核心基因组的系统发育、种群结构分析和ANI结果对地衣虫进行评价。比较基因组分析揭示了b。副苔藓虫有助于其在根际的共生生活方式，包括一个开放的pan基因组，碳水化合物和氨基酸的运输和代谢的多样性。在插入序列、前噬菌体、基因组岛和次生代谢合成酶操纵子的数量和位置上，两种菌株存在显著差异。paralicheniformisandB。地衣芽。特别是丰霉素、杆菌肽和蓝肽的大部分基因簇只存在于b中。通过水平基因转移（HGT）方法获得了副苔藓虫群（paricheniformisisand），这些簇可作为区分b。paralicheniformisandB。地衣芽。结论MDJK30和其他菌株在遗传水平上具有促进植物生长的性状，可以作为PGPR进行开发和商业化应用。核心基因组系统发育和群体结构分析已被证明是鉴别b。paralicheniformisandB。地衣芽。比较基因组分析说明了副青衣虫-地衣虫群在根际适应方面的遗传差异。
BackgroundMembers of the genusBacillusare important plant growth-promoting rhizobacteria that serve as biocontrol agents.Bacillus paralicheniformisMDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship betweenB. paralicheniformisandB. licheniformis.ResultsA comparative genomics analysis based onB. paralicheniformisMDJK30 and 55 other previously reportedBacillusstrains was performed. The evolutionary position of MDJK30 and the evolutionary relationship betweenB. paralicheniformisandB. licheniformiswere evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features ofB. paralicheniformisthat contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons betweenB. paralicheniformisandB. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present inB. paralicheniformisand were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishingB. paralicheniformisandB. licheniformis.ConclusionsThis study reveals that MDJK30 and the other strains of lineageparalicheniformispresent plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiatingB. paralicheniformisandB. licheniformis. Comparative genomic analyses illustrate the genetic differences between theparalicheniformis-licheniformisgroup with respect to rhizosphere adaptation.