Structure and evolution of the r/b chromosomal regions in rice, maize, and sorghum

Sequence data from this article have been deposited with the GenBank Data Libraries under accession nos.: AY542311; million years ABSTRACT The r1 and b1 genes of maize, each derived from the chromosomes of two progenitors that hybridized more than 4.8 million years ago (mya), have been a rich source for studying transposition, recombination, genomic imprinting, and paramutation. To provide a phylogenetic context to the genetic studies, we sequenced orthologous regions from maize and sorghum (>600 kb) surrounding these genes and compared them with the rice genome. This comparison showed that the homoeologous regions underwent complete or partial gene deletions, selective retention of orthologous genes, and insertion of non-orthologous genes. Phylogenetic analyses of the r/b genes revealed that the ancestral gene was amplified independently in different grass lineages, that rice experienced an intragenomic gene movement and parallel duplication, that the maize r1 and b1 genes are descendants of two divergent progenitors, and that the two paralogous r genes of sorghum are almost as old as the sorghum lineage. Such sequence mobility also extends to linked genes. The cisZOG genes are characterized by gene amplification in an ancestral grass, parallel duplications and deletions in different grass lineages, and movement to a nonorthologous position in maize. In contrast to gene mobility, transpositions occurred mostly in the maize and rice regions recently (<3 mya). region the Rph7 region and the lrs/lg Although these studies generally confirmed gene conservation (microcollinearity) among orthologous segments of various grass taxa, they also reported small-scale genic rearrangements, such as gene insertions, deletions, amplifications, inversions and translocations. In this study, we present a comparison of genomic content of orthologous chromosomal regions containing the r/b gene homologs from rice, maize, and sorghum. We examine which types of genome evolution resulted in the observed genomic structure of these regions across the three species and between the two duplicated (homoeologous) regions of maize. We present a detailed analysis of molecular evolution of the r/b gene family in grasses and examine the evolutionary pattern of gene duplication of the tightly linked cis-zeatin O-glucosyltransferase ( cisZOG ) gene. We also examine the content and history of retrotransposition within these regions.