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

Eric Lyons, Michael Freeling

Research output: Contribution to journalArticlepeer-review

352 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)661-673
Number of pages13
JournalPlant Journal
Issue number4
StatePublished - Feb 2008


  • CNS
  • Fractionation
  • Plant comparative genomics
  • Synteny

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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