Dataset Information

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes.

ABSTRACT: The sequences of large insert clones containing genomic DNA that is orthologous to the maize adh1 region were obtained for sorghum, rice, and the adh1-homoeologous region of maize, a remnant of the tetraploid history of the Zea lineage. By using all four genomes, it was possible to describe the nature, timing, and lineages of most of the genic rearrangements that have differentiated this chromosome segment over the last 60 million years. The rice genome has been the most stable, sharing 11 orthologous genes with sorghum and exhibiting only one tandem duplication of a gene in this region. The lineage that gave rise to sorghum and maize acquired a two-gene insertion (containing the adh locus), whereas sorghum received two additional gene insertions after its divergence from a common ancestor with maize. The two homoeologous regions of maize have been particularly unstable, with complete or partial deletion of three genes from one segment and four genes from the other segment. As a result, the region now contains only one duplicated locus compared with the eight original loci that were present in each diploid progenitor. Deletion of these maize genes did not remove both copies of any locus. This study suggests that grass genomes are generally unstable in local genome organization and gene content, but that some lineages are much more unstable than others. Maize, probably because of its polyploid origin, has exhibited extensive gene loss so that it is now approaching a diploid state.

SUBMITTER: Ilic K

PROVIDER: S-EPMC218747 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes.

Ilic Katica K SanMiguel Phillip J PJ Bennetzen Jeffrey L JL

Proceedings of the National Academy of Sciences of the United States of America 20031006 21

The sequences of large insert clones containing genomic DNA that is orthologous to the maize adh1 region were obtained for sorghum, rice, and the adh1-homoeologous region of maize, a remnant of the tetraploid history of the Zea lineage. By using all four genomes, it was possible to describe the nature, timing, and lineages of most of the genic rearrangements that have differentiated this chromosome segment over the last 60 million years. The rice genome has been the most stable, sharing 11 ortho ...[more]

PMID: 14530400

Similar Datasets

Project description:BackgroundThe potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns.ResultsThe most apparent pattern observed was the occurrence of spatially conserved 'core modules' among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as 'regulatory fine-tuners' and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis.ConclusionsPatterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.

Dataset Information

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes.

Publications

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets