How to usefully compare homologous plant genes and chromosomes as DNA sequences

被引：352

作者：

Lyons, Eric ^{[1
]}

Freeling, Michael ^{[1
]}

机构：

[1] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

来源：

PLANT JOURNAL | 2008年 / 53卷 / 04期

关键词：

plant comparative genomics; CNS; synteny; fractionation;

D O I：

10.1111/j.1365-313X.2007.03326.x

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.

引用

页码：661 / 673

页数：13

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