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

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.