基因组时代线粒体基因组拼装策略及软件应用现状  

Mitogenome assembly strategies and software applications in the genome era

作　　者：匡卫民 于黎[1] Weimin Kuang;Li Yu(State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan,School of Life Sciences,Yunnan University,Kunming 650091,China)

机构地区：[1]云南大学生命科学学院省部共建生物资源保护与利用国家重点实验室

出　　处：《遗传》2019年第11期979-993,共15页Hereditas（Beijing)

基　　金：国家自然科学基釐项目(编号：31872213);云南省教育厅科学研究基釐产业化培育项目(编号：2016CYH02);云南省研究生学术新人奖资助项目~~

摘　　要：随着测序技术的不断发展,越来越多物种的全基因组数据被测定和广泛应用。在二代基因组数据爆发式增长的同时,除了核基因组数据,线粒体基因组数据也非常重要。高通量测序的全基因组序列中除了核基因组序列也包括线粒体基因组序列,如何从海量的全基因组数据中提取和拼装线粒体基因组序列并加以应用成为线粒体基因组在分子生物学、遗传学和医学等方面的研究方向之一。基于此,从全基因组数据中提取线粒体基因组序列的策略及相关的软件不断发展。根据从全基因组数据中锚定线粒体reads的方式和后续拼装策略的不同,可以分为有参考序列拼装方法和从头拼装方法,不同拼装策略及软件也表现出各自的优势和局限性。本文总结并比较了当前从全基因组数据中获得线粒体基因组数据的策略和软件应用,并对使用者在使用不同策略和相关软件方面给予建议,以期为线粒体基因组在生命科学的相关研究中提供方法上的参考。With rapid advances in next-generation sequencing technologies, the genomes of many organisms have been sequenced and widely applied in different settings. Mitochondrial genome data is equally important and the high-throughput whole-genome data typically contain mitochondrial genome(mitogenome) sequences. How to extract and assemble the mitogenome from massive whole-genome sequencing(WGS) data remain a hot area in molecular biology, genetics and medicine. The cataloging and analysis of accumulating mitogenome data promotes the development of assembly strategies and corresponding software applications related to mitochondrial DNA from the WGS data. Mitogenome assembly strategies can be divided into mitogenome-reference strategy and de novo strategy. Each strategy has different advantages and limitations with respect to the difference of bait mitogenome-linked short reads from the WGS data and corresponding assembly strategy. In this review, we summarize and compare current mitogenome assembly strategies and the software applications available. We also provide suggestions related to use different assembly strategies and software applications, and the expected benefits and limitations of methods references in life science.

关 键 词：全基因组 线粒体基因组 有参考序列拼装方法 从头拼装方法 拼装软件 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]