一株太平洋表层海水来源阿拉伯海假交替单胞菌N1230-9的全基因组测序及比较基因组学分析

Genome sequencing and comparative genomic analysis of Pseudoalteromonas arabiensis N1230-9 isolated from the surface seawater of the Pacific Ocean

摘要:

【目的】阐述阿拉伯海假交替单胞菌(Pseudoalteromonas arabiensis)的分子进化与生态适应策略。【方法】借助Illumina HiSeq X Ten和Oxford Nanopore PromethION测序平台对一株分离自太平洋表层海水的菌株Pseudoalteromonas arabiensis N1230-9进行全基因组测序，利用相关生物信息学分析软件对原始数据进行组装和基因组注释，并与一株分离自深海沉积物环境的模式菌株Pseudoalteromonas arabiensis JCM 17292进行比较基因组分析。【结果】菌株N1230-9基因组由2条染色体组成，基因组大小为4 627 470 bp，G+C含量为40.85%，共编码4 202个蛋白。功能基因注释结果显示，菌株N1230-9具有适应海洋环境的多种类型功能基因，包括重金属抗性基因、多种铁离子摄取系统编码基因、多种噬菌体防御系统编码基因、种类丰富的水解酶编码基因、多种碳水化合物代谢相关基因，以及数量众多的二元信号传导系统编码基因。通过比较基因组分析发现，菌株N1230-9和菌株JCM 17292拥有适应不同生态位的特有基因，这些基因主要涉及血红素摄取、重金属抗性、噬菌体防御、二元信号系统传导和横向基因水平转移。【结论】来自表层海水的菌株P. arabiensis N1230-9已演化出了适应其生态位的特有基因。

Abstract:

[Objective] To detail the molecular evolution and ecological adaptation of Pseudoalteromonas arabiensis. [Methods] Illumina HiSeq X Ten and Oxford Nanopore PromethION were used for the whole genome sequencing of Pseudoalteromonas arabiensis N1230-9 isolated from the surface seawater of the Pacific Ocean. Bioinformatics tools were used to assemble and annotate the original sequencing data, and the type strain Pseudoalteromonas arabiensis JCM 17292 was used for comparative genomic analysis. [Results] The genome of strain N1230-9 consisted of two chromosomes, with a size of 4 627 470 bp and the G+C content of 40.85%, encoding a total of 4 202 proteins. Genome annotation showed that strain N1230-9 carried functional genes contributing to the adaption to the marine environment. These genes were mainly involved in heavy metal resistance, iron-uptake systems, anti-phage defense systems, hydrolytic enzymes, carbohydrate metabolism, and two-component signaling systems. Comparative genomic analysis revealed that strain N1230-9 and strain JCM 17292 possessed unique genes conferring adaption to different ecological niches. These genes were primarily involved in heme uptake, heavy metal resistance, anti-phage defense, two-component signaling, and horizontal gene transfer. [Conclusion] P. arabiensis N1230-9 isolated from surface seawater has evolved unique genes for adaption to its ecological niche.