34株假单胞菌的泛基因组分析  

Pan-genomic characteristic of 34 Pseudomonas strains

作　　者：方源 谢柏盛 黄婷 郑鑫 许子牧 汪家权[1] FANG Yuan;XIE Baisheng;HUANG ting;ZHENG Xin;XU Zimu;WANG Jiaquan(School of Resources and Environmental Engineering,Hefei University of Technology,Hefei 230009,China;College of Engineering,Peking University,Beijing 100871,China)

机构地区：[1]合肥工业大学资源与环境工程学院,合肥230009 [2]北京大学工学院,北京100871

出　　处：《应用与环境生物学报》2021年第4期1031-1038,共8页Chinese Journal of Applied and Environmental Biology

基　　金：国家自然科学基金青年科学基金项目(51807046)资助。

摘　　要：假单胞菌属在各种环境广泛分布且具有重要的生态应用价值,然而当前研究对其环境适应性遗传基础的解析尚不充分.选择33株有效发表且具有全基因组序列以及一株新分离的假单胞菌的全基因组进行泛基因组学分析.结果表明,选择的假单胞菌属菌株泛基因组含有173271条蛋白序列,共有30847个同源基因家族,包括1505个核心基因,基因组呈开放型.通过分析不同基因组的基因组演化特征,发现通过基因水平转移获得的基因占整个基因组的比例为32%-48%,其平均基因岛数量为53个.发现假单胞菌属泛基因组的开发性与其频繁的基因水平转移事件和快速的基因进化有关.进一步分析表明,不同基因组中的功能基因家族按照菌株的环境分布进行聚类,表明对特殊环境的适应决定了假单胞菌的遗传特征.本研究初步揭示了假单胞菌属细菌遗传特征的共性与特性,结果可为解析假单胞菌属环境适应性的遗传基础与功能多样性的演化发生机制提供研究线索.Members of the Pseudomonas spp.family are widely distributed in various environments and have important ecological application potential.However,the genetic basis of their environmental adaptation remains unclear.In this work,we performed pan-genomic analysis of Pseudomonas based on 33 complete genomes from Gen Bank and an additional genome of a newly isolated Pseudomonas strain.The results show that the 34 Pseudomonas strains have a pan-genome consisting of 173271 predicted genes grouped into 30847 homologous gene families,including a core genome consisting of 1505 genes.The pan-genome of the studied Pseudomonas strains is open,which may be due to the combined effects of horizontal gene transfer(HGT)and rapid evolution.Approximately 32%-48%of genes in Pseudomonas genomes are obtained through HGT,and the average number of genomic islands is 53 per genome.Further analyses showed that functional gene families in different genomes were clustered according to their isolation environments,which indicates that adaptation to a special environment determines the genetic characteristics of Pseudomonas.This study revealed the genetic characteristics of Pseudomonas strains and provided clues for the genetic basis of environmental adaptation and the evolutionary mechanisms of functional diversity.

关 键 词：假单胞菌属 泛基因组 核心基因组 环境适应 

分 类 号：Q933[生物学—微生物学]