How to usefully compare homologous plant genes and chromosomes as DNA sequences
Article first published online: 4 FEB 2008
© 2008 The Authors
The Plant Journal
Volume 53, Issue 4, pages 661–673, February 2008
How to Cite
Lyons, E. and Freeling, M. (2008), How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal, 53: 661–673. doi: 10.1111/j.1365-313X.2007.03326.x
- Issue published online: 4 FEB 2008
- Article first published online: 4 FEB 2008
- Received 1 June 2007; revised 11 September 2007; accepted 17 September 2007.
- plant comparative genomics;
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.