Conservation, Rearrangement, and Deletion of Gene Pairs During the Evolution of Four Grass Genomes

• Published in: DNA research Vol. 17; no. 6; pp. 343 - 352
• Main Authors: Krom, N., Ramakrishna, W.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.12.2010
• Subjects: Biological and medical sciences; Brachypodium; Brachypodium - genetics; Conserved Sequence; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Gene Deletion; Gene Order; Gene Rearrangement; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Molecular and cellular biology; Molecular genetics; Oryza - genetics; Oryza sativa; Poaceae - genetics; Sequence Analysis, DNA; Sorghum; Sorghum - genetics; Zea mays; Zea mays - genetics; Chromosomal aberration; Molecular evolution; Gene; Coexpression; Conservation; Gene rearrangement; Deletion; gene pairs; Genetics; grass genomes; Genome; rearrangement
• ISSN: 1340-2838; 1756-1663; 1756-1663
• DOI: 10.1093/dnares/dsq022

Gene order and content differ among homologous regions of closely related genomes. Similarities in the expression profiles of physically adjacent genes suggest that the proper functioning of these genes depends on maintaining a specific position relative to each other. To better understand the results of the interaction of these two genomic forces, convergent, divergent, and tandem gene pairs in rice and sorghum, as well as their homologs in rice, sorghum, maize, and Brachypodium were analyzed. The status of each pair in all four species: whether it was conserved, inverted, rearranged, or missing homologs was determined. We observed that divergent gene pairs had lower rates of conservation than convergent or tandem pairs, but higher rates of rearranged pairs and missing homologs in maize than in any other species. We also discovered species-specific gene pairs in rice and sorghum. In rice, gene pairs with strongly correlated expression levels were conserved significantly more often than those with little or no correlation. We assigned three types of gene pair to one of 14 possible evolutionary history categories to uncover their evolutionary dynamics during the evolution of grass genomes.