基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用

doi:10.16288/j.yczz.15-038

遗传 ›› 2015, Vol. 37 ›› Issue (7): 702-710.doi: 10.16288/j.yczz.15-038

基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用

方翔, 李宁求, 付小哲, 李凯彬, 林强, 刘礼辉, 石存斌, 吴淑勤

中国水产科学研究院珠江水产研究所,农业部渔用药物创制重点实验室,广东省水产动物免疫技术重点实验室,广州 510380

收稿日期:2015-01-16 修回日期:2015-04-01 出版日期:2015-07-20 发布日期:2015-07-20
通讯作者: 李宁求,副研究员,研究方向：水产病害。E-mail: liningq@126.com;
吴淑勤,研究员,研究方向：水产病害。E-mail: wushuqing001@21cn.com
作者简介:方翔,助理研究员,研究方向：水产生物信息学。E-mail: wayj86@gmail.com
基金资助:
广州市珠江科技新星专项(编号: 2012J2200078)和中国水产科学研究院院级中央级公益性科研院所基本科研业务费(编号: 2013A0609)资助

Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer

Xiang Fang, Ningqiu Li, Xiaozhe Fu, Kaibin Li, Qiang Lin, Lihui Liu, Cunbin Shi, Shuqin Wu

Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China

Received:2015-01-16 Revised:2015-04-01 Online:2015-07-20 Published:2015-07-20

摘要/Abstract

摘要： 作为生命科学的关键组成,生物信息学已被广泛地应用于基因组学、转录组学和蛋白质组学中。然而,生物信息分析平台的构建需要高性能计算机而非普通的个人电脑,从而极大地限制了生物信息学在水产科学中的应用。本研究基于“天河二号”超级计算机,构建了水产病原生物信息分析平台。该平台由基因组与转录组测序数据分析、蛋白质结构预测和分子动力学模拟3个功能模块组成。为了验证该平台的实用性,以水生动物病原微生物为例进行了生物信息学分析。通过Blast检索、GO和InterPro注释,鉴定了约氏黄杆菌(Flavobacterium johnsoniae)M168株的功能基因并对其进行了注释。通过同源模建,构建了草鱼呼肠孤病毒(Grass carp reovirus,GCRV)HZ-08的5个小节段的蛋白结构模型。对嗜水气单胞菌(Aeromonas hydrophila)外膜蛋白A进行了分子动力学模拟,并观察了平衡过程中系统温度、总能量、均方根偏差和环区构象的变化。以上结果均显示本研究成功建立了在“天河二号”超级计算机上运行的水产病原生物信息分析平台。此项研究将为其他学科生物信息分析平台的构建提供思路和线索。

关键词: 生物信息学, 天河二号, 水产病原

Abstract: As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects.

Key words: bioinformatics, MilkyWay-2, aquatic pathogen

方翔, 李宁求, 付小哲, 李凯彬, 林强, 刘礼辉, 石存斌, 吴淑勤. 基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用[J]. 遗传, 2015, 37(7): 702-710.

Xiang Fang, Ningqiu Li, Xiaozhe Fu, Kaibin Li, Qiang Lin, Lihui Liu, Cunbin Shi, Shuqin Wu. Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer[J]. HEREDITAS(Beijing), 2015, 37(7): 702-710.

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基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用

Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer

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