系统发育基因组学研究进展

doi:10.3724/SP.J.1005.2014.0669

遗传 ›› 2014, Vol. 36 ›› Issue (7): 669-678.doi: 10.3724/SP.J.1005.2014.0669

系统发育基因组学研究进展

王章群¹, 解增言², 蔡应繁³, 舒坤贤², 黄飞飞²

1. 重庆邮电大学计算机科学与技术学院, 重庆 400065;
2. 重庆邮电大学生物信息学院, 重庆 400065;
3. 河南大学生命科学学院, 开封 475001

收稿日期:2013-10-28 出版日期:2014-07-20 发布日期:2014-06-23
通讯作者: 解增言, 讲师, 博士, 硕士生导师, 研究方向：生物信息学和分子进化。E-mail: zengyanxie@gmail.com 蔡应繁, 教授, 博士, 博士生导师, 研究方向：植物分子生物学和生物信息学。E-mail: cyf@henu.edu.cn
作者简介:王章群, 硕士研究生, 专业方向：生物信息学。Tel: 023-62461048; E-mail: 515544361@qq.com
基金资助:
国家自然科学基金项目(编号：31071461)和重庆邮电大学博士启动基金项目(编号：A2009-18, A2011-01)资助

Advances in phylogenomics

Zhangqun Wang¹, Zengyan Xie², Yingfan Cai³, Kunxian Shu², Feifei Huang²

1. College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing 400065, China;
2. College of Bio-information, Chongqing University of Posts and Telecommunications, Chongqing 400065, China;
3. School of Life Science, Henan University, Kaifeng 475001, China

Received:2013-10-28 Online:2014-07-20 Published:2014-06-23

摘要/Abstract

摘要： 系统发育基因组学是利用全基因组数据构建系统发育树的新领域。全基因组数据能有效消除横向基因转移和类群间基因进化速率差异等因素对系统发育树的影响。根据所使用的全基因组数据的类型, 可以将系统发育基因组学方法分为以下5类：多基因联合建树方法, 基于基因含量的方法, 基于基因排列信息的方法, 基于序列短串含量特征信息的方法及基于代谢途径的方法。文章系统地总结了每一类方法的原理、速度、准确性、适用范围及在各个生物类群中的应用, 并对系统发育基因组学的前景及面临的挑战进行了概述。

关键词: 系统发育, 系统发育树, 系统发育基因组学, 基因含量, 序列短串

Abstract: Phylogenomics is a new phylogenetic field that aims to rebuild phylogenetic relationship of organisms using whole genome data. It can effectively eliminate the impact of horizontal gene transfer and variant evolutionary rates on phylogeny. According to the genome data type they are based on, these methods can be classified into five groups: multi-gene based, gene content based, gene order based, K-string based, and metabolic pathway based. The mechanism, speed, accuracy, applicable range and their application of these methods are summarized. The prospects of phylogenomics and challenges that it is faced with are also discussed.

Key words: phylogeny, phylogenetic tree, phylogenomics, gene content, K-string

王章群, 解增言, 蔡应繁, 舒坤贤, 黄飞飞. 系统发育基因组学研究进展[J]. 遗传, 2014, 36(7): 669-678.

Zhangqun Wang, Zengyan Xie, Yingfan Cai, Kunxian Shu, Feifei Huang. Advances in phylogenomics[J]. HEREDITAS(Beijing), 2014, 36(7): 669-678.

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系统发育基因组学研究进展

Advances in phylogenomics

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