基因组时代线粒体基因组拼装策略及软件应用现状

doi:10.16288/j.yczz.19-227

遗传 ›› 2019, Vol. 41 ›› Issue (11): 979-993.doi: 10.16288/j.yczz.19-227

• 综述 • 下一篇

基因组时代线粒体基因组拼装策略及软件应用现状

匡卫民, 于黎()

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,昆明 650091

收稿日期:2019-08-07 修回日期:2019-09-25 出版日期:2019-11-20 发布日期:2019-10-15
通讯作者: 于黎 E-mail:yuli@ynu.edu.cn
作者简介:匡卫民,博士,专业方向：遗传学。E-mail: kuangwm0714@sina.com
基金资助:
国家自然科学基金项目编号：(31872213);云南省教育厅科学研究基金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

Mitogenome assembly strategies and software applications in the genome era

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

Received:2019-08-07 Revised:2019-09-25 Online:2019-11-20 Published:2019-10-15
Contact: Yu Li E-mail:yuli@ynu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31872213);Industrialization Cultivation Project of Scientific Research Fund of Yunnan Education Department No(2016CYH02);and the Academic Graduate Students Foundation of Yunnan Province

摘要/Abstract

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。

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

Abstract:

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.

Key words: whole-genome sequencing, mitogenome, mitogenome-reference assembly, de novo assembly, assembly software

匡卫民, 于黎. 基因组时代线粒体基因组拼装策略及软件应用现状[J]. 遗传, 2019, 41(11): 979-993.

Weimin Kuang, Li Yu. Mitogenome assembly strategies and software applications in the genome era[J]. Hereditas(Beijing), 2019, 41(11): 979-993.

图/表 2

图1

表1

线粒体基因组拼装软件信息"

软件名称	是否需要参考序列/ 参考序列类型	适用物种	输入文件格式、类型	变异注释	结构可视化	运行环境	编程语言	软件网址
MIA	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	C/C++	https://github.com/mpieva/mapping-iterative-assembler
MitoBamAnnotator	是/ rCRS	人	Bam	√	√	Web	Java	http://bioinfo.bgu.ac.il/bsu/software/MITO-BAM
MitoSeek	是/rCRS和hg19	人	Bam	√	×	GUI	Perl	https://github.com/riverlee/MitoSeek
mtDNA- profiler	是/rCRS	人	Fasta	×	√	Web	Java	http://mtprofiler.yonsei.ac.kr
MITObim	是/自定义参考序列	任意物种	Bam	×	×	CUI	Perl	https://github.com/chrishah/MITObim
Mit-o-matic	是/rCRS	人	Fastq、SE reads和 PE reads	√	√	Web/GUI	Java	http://genome.igib.res.in/mitomatic
MToolBox	是/rCRS和RSRS	人	Fastq/Bam/Sam、 SE reads和PE reads	√	×	Web/CUI	Python	https://sourceforge.net/projects/mtoolbox
ARC	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	Web/CUI	Python	https://github.com/ibest/ARC
Phy-Mer	是/自定义参考序列	任意物种	Fasta/fastq/Bam、 SE reads和PE reads	×	√	CUI	Python	https://github.com/danielnavarrogomez/phy-mer
mtDNA- Server	是/rCRS和RSRS	人	Fastq/Bam/VCF、 SE reads和PE reads	√	√	Web	Java	https://mtdna-server.uibk.ac.at
IOGA	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://github.com/holmrenser/IOGA
NOVOPlasty	是/自定义参考序列	任意物种	Fastq/fasta、SE reads 和PE reads	×	×	Web/CUI	Perl	https://github.com/ndierckx/NOVOPlasty
Norgal	否	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python/ Java	https://bitbucket.org/kosaidtu/norgal
Organelle- PBA	是/自定义参考序列	任意物种	PacBio reads	×	×	CUI	Perl	https://github.com/aubombarely/Organelle_PBA
MitoSuite	是/rCRS, RSRS, hg19, GRCh37和38	人	Bam/Sam	√	√	GUI	Python	https://mitosuite.com
ORG.Asm	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://git.metabarcoding.org/org-asm/org-asm
MitoZ	否	任意物种	Fastq、SE reads和 PE reads	√	√	CUI	Python	https://github.com/linzhi2013/MitoZ
GetOrganelle	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://github.com/Kinggerm/GetOrganelle
Trimitomics	是/自定义参考序列	任意物种	RNA-seq reads、 PE reads	×	×	Unknown	Unknown	Unknown

表1

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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

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