title: Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes.
abstract: Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis. General microcolinearity was observed for the four shared genes in this region. However, three genic rearrangements were observed. First, the rice region contains a cluster of 48 predicted small nucleolar RNA genes, but the comparable region from sorghum contains no homologous loci. Second, gene 2 was inverted in the barley lineage by an apparent unequal recombination after the ancestors of barley and wheat diverged, 11-15 million years ago (mya). Third, gene 4 underwent direct tandem duplication in a common ancestor of barley and wheat 29-41 mya. All four of the shared genes show the same synonymous substitution rate, but nonsynonymous substitution rates show significant variations between genes 4a and 4b, suggesting that gene 4b was largely released from the strong purifying selection that acts on gene 4a in both barley and wheat. Intergenic retrotransposon blocks, many of them organized as nested insertions, mostly account for the lower gene density of the barley and wheat regions. All but two of the retrotransposons were found in the regions between genes, while all but 2 of the 51 inverted repeat transposable elements were found as insertions in genic regions and outside the retrotransposon blocks.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
authors.forename: Wusirika
authors.initials: W
authors.lastname: Ramakrishna
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
authors.forename: Yong-Jin
authors.initials: YJ
authors.lastname: Park
authors.forename: Carlos
authors.initials: C
authors.lastname: Busso
authors.forename: John
authors.initials: J
authors.lastname: Emberton
authors.forename: Phillip
authors.initials: P
authors.lastname: SanMiguel
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
mesh_terms: D005075:Biological Evolution; D022202:Chromosomes, Artificial, Bacterial; D004251:DNA Transposable Elements; D002523:Edible Grain / Q000235:genetics*; D018745:Genome, Plant; D008969:Molecular Sequence Data; D017354:Point Mutation; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements