基于基因组的产铁载体海洋嗜盐菌JSM 21308的系统发育分析

doi:10.13438/j.cnki.jdzk.2024.05.008

吉首大学学报（自然科学版） ›› 2024, Vol. 45 ›› Issue (5): 61-67.DOI: 10.13438/j.cnki.jdzk.2024.05.008

基于基因组的产铁载体海洋嗜盐菌JSM 21308的系统发育分析

邓丽颖，石愿杰，陈锦华，达春瑶，刘祝祥，陈义光

（1.张家界学院医学院，湖南张家界 427000；2.吉首大学生物资源与环境科学学院，湖南吉首 416000）

出版日期:2024-09-25 发布日期:2024-11-08
作者简介:邓丽颖（1995—），女，湖南张家界人，张家界学院医学院助教，硕士，主要从事微生物资源与多样性研究
基金资助:
湖南省教育厅科技项目（22A0770）；湖南省研究生科研创新项目（CX20231081）；吉首大学校级科研项目（JDY22072）

Genome Based Phylogeny Analysis of Siderophore-Producing Marine Halophilic Bacterium JSM 21308

DENG Liying,SHI Yuanjie,CHEN Jinhua,DA Chunyao,LIU Zhuxiang,CHEN Yiguang

(1.School of Medicine,Zhangjiajie College,Zhangjiajie 427000,Hunan China;2.College of Biology and Environmental Sciences,Jishou University,Jishou 416000,Hunan China)

Online:2024-09-25 Published:2024-11-08

摘要/Abstract

摘要：为了确定分离自海南红树林沉积物的产铁载体嗜盐菌JSM 21308的系统分类地位，采用16S rRNA基因序列分析方法初步确定菌株的系统进化地位，测定基因组框架图，再采用比较基因组学技术分析该菌株与其系统发育关系密切的已知物种典型菌株之间的GC摩尔分数、平均核苷酸一致性（ANI）和数字DNA-DNA杂交值（dDDH），并进行基因组系统发育学分析，以更准确地判定菌株JSM 21308与密切相关的典型菌株的系统发育关系.16S rRNA基因序列分析表明，菌株JSM 21308应归属于芽孢杆菌科（Bacillaceae），与该科中假嗜碱芽孢杆菌属（Pseudalkalibacillus）的P. hwajinpoensis SW-72^T和嗜盐碱芽孢杆菌属（Alkalihalobacillus）的A. hemicentroti JSM 076093T的系统发育关系最为密切，它们之间的16S rRNA基因序列相似性分别为99.66%和98.96%，高于原核生物物种界限阈值98.7%，但JSM 21308在基于16S rRNA基因序列的系统发育树上形成独立进化分支.比较基因组学分析发现，菌株JSM 21308与P. hwajinpoensis SW-72T的ANI值、dDDH值分别为77.69%，21.40%，而与A. hemicentroti JSM 076093T的ANI值、dDDH值分别高达99.99%，100%，明显高于普遍认可的细菌物种划分的阈值（ANI 95%~96%，dDDH 70%）.基于全基因组序列的系统发育分析结果显示，JSM 21308与A. hemicentroti JSM 076093T属于同一分类单元（物种）.显然，结合16S rRNA基因序列的系统发育和比较基因组学分析结果判断，菌株JSM 21308应归属于嗜盐碱芽孢杆菌属，可鉴定为该属已知物种A. hemicentroti的一个新成员.

关键词： 海洋嗜盐菌, 基因组框架图, 比较基因组学, 系统发育, 嗜盐碱芽孢杆菌属

Abstract: To accurately determine the systematic status of the siderophore-producing marine halophilic bacteria JSM 21308 isolated from mangrove sediment collected from the Moon Bay in Wenchang City in Hainan Province,PR China,the evolutionary status was primarily analysed based on 16S rRNA gene sequences.The draft genome was mapped,and then the exact phylogenetic relationship of strain JSM 21308 with its closely relative type strains was investigated by comparative genomics analysis based on whole-genome sequences,including comparisons of G+C content,average nucleotide identity (ANI),and digital DNA-DNA hybridization (dDDH) values,and phylogenomic analysis.The result of 16S rRNA gene sequence analysis showed that JSM 21308 belonged to the family Bacillaceae,and was most closely related to Pseudalkalibacillus hwajinpoensis SW-72^T (16S rRNA gene sequence similarity,99.66%) and Alkalihalobacillus hemicentroti JSM 076093^T (98.7%).These three strains formed obvious subclusters on the phylogenetic tree of 16S rRNA gene sequence,in which JSM 21308 made a separated branch.The results of comparative genomics analysis showed that the ANI and dDDH values of strain JSM 21308 and the type strain of A. hemicentroti were respectively 77.69% and 21.40%,all lower than the generally recognized threshold of bacterial species (ANI,95%~96%;dDDH,70% ).However,the ANI and dDDH values of strain JSM 21308 and A. hemicentroti JSM 076093^T reached up to 99.99% and 100%,respectively.The result of phylogenomic analysis performed at the species level (70% dDDH threshold ) and subspecies level (79% dDDH threshold) also showed that strain JSM 21308 and the type strain of A. hemicentrotinot only represented the same species cluster but also the same subspecies cluster.Based on the combination of both the results of phylogenetic analysis of 16S rRNA gene sequences and comparative genomic analysis,strain JSM 21308 should be a new member of the known species of the genus Alkalihalobacillus,A. hemicentroti.

Key words: marine halophilic bacterium, draft genome, comparative genomics, phylogeny, Alkalihalobacillus

邓丽颖, 石愿杰, 陈锦华, 达春瑶, 刘祝祥, 陈义光. 基于基因组的产铁载体海洋嗜盐菌JSM 21308的系统发育分析[J]. 吉首大学学报（自然科学版）, 2024, 45(5): 61-67.

DENG Liying, SHI Yuanjie, CHEN Jinhua, DA Chunyao, LIU Zhuxiang, CHEN Yiguang. Genome Based Phylogeny Analysis of Siderophore-Producing Marine Halophilic Bacterium JSM 21308[J]. Journal of Jishou University(Natural Sciences Edition), 2024, 45(5): 61-67.

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基于基因组的产铁载体海洋嗜盐菌JSM 21308的系统发育分析

Genome Based Phylogeny Analysis of Siderophore-Producing Marine Halophilic Bacterium JSM 21308

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