Maize GEvo: A comparative DNA sequence alignment visualization and research tool

Eric Lyons, Sara Castelletti, Brent Pedersen, Damon Lisch, Michael Freeling

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Comparing the DNA sequence of maize genes and chromosomal regions to their maize homeologs and to other grass orthologs provides a quick check for many annotation errors and may identify useful regions of conservation and divergence. Fractionation and subfunctionalization, two processes that shape the evolution of genes and genomes, may be evaluated by comparing syntenic chromosomal regions within and among genomes. We provide an overview of maize's genome evolution, emphasizing the processes of fractionation and subfunctionalization. We then provide a tutorial of our software for multiple DNA sequence alignment display and analysis. As an example, we begin with one maize gene sequence, find a pair of maize home-ologous gene regions, and add an orthologous segment from sorghum and rice; we then analyze this 4-way DNA alignment.

Original languageEnglish (US)
Title of host publicationHandbook of Maize
Subtitle of host publicationGenetics and Genomics
PublisherSpringer New York
Pages341-351
Number of pages11
ISBN (Electronic)9780387778631
ISBN (Print)9780387778624
DOIs
StatePublished - Jan 1 2009
Externally publishedYes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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  • Cite this

    Lyons, E., Castelletti, S., Pedersen, B., Lisch, D., & Freeling, M. (2009). Maize GEvo: A comparative DNA sequence alignment visualization and research tool. In Handbook of Maize: Genetics and Genomics (pp. 341-351). Springer New York. https://doi.org/10.1007/978-0-387-77863-1_17