Comparative sequence analysis of MONOCULM1 -orthologous regions in 14 Oryza genomes

Abstract

Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.comparative genomics ͉ genome evolution ͉ microcolinearity ͉ allotetraploid ͉ conserved noncoding sequence

Rapid diversification of five Oryza AA genomes associated with rice adaptation

“…2A and SI Appendix, Fig. S10), consistent with previous results (18)(19)(20). Nevertheless, there were still a number of microstructural changes, including lineage-specific differences that were concordant with the known phylogenetic relationships and random fluctuations in TE biology (SI Appendix, Tables S20 and S21).…”

“…We estimated an overall extent of genome divergences between SAT and the other five AA-genome Oryza species by randomly sampling 103 segments totaling ∼15 Mb, with an average length of ∼100 kb (∼3.9% of the rice genome). Global genome divergences between genomic segments supported their phylogenetic positions in the topology but far exceeded orthologous gene sequence variation (SI Appendix, Table S19), indicating that differential TE insertion and turnover histories in the intergenic regions account for most of the sequence divergence (19,29).…”

“…By placing multiple Oryza genome comparisons in a phylogenetic context, previous studies have recorded some of the genomic changes associated with the diversification of the rice genus (16)(17)(18)(19)(20). Several studies have compared orthologous genomic segments of Oryza species that represent the different genome types that have diverged over long time scales (18)(19)(20).…”

“…Several studies have compared orthologous genomic segments of Oryza species that represent the different genome types that have diverged over long time scales (18)(19)(20). However, none of these analyses provide the full-genome, multispecies perspective that allows comprehensive analysis of gene, genome, or trait evolution.…”

The Future of Rice Genomics: Sequencing the Collective Oryza Genome

“…The remaining 16 wild species (including both diploid and tetraploid species) are classified into nine other genome types. Figures 1 and 2 show a phylogenetic tree of the genus Oryza (inferred from Ge et al 1999;Lu et al 2009 andAmmiraju et al 2010) and a photograph of the diploid Oryza species at the same developmental stage, respectively. The wild Oryza species offer a largely untapped resource of genes that have the potential to solve many of the world's rice production issues, including yield, drought and salt tolerance, and disease and insect resistance Khush 1997, 2003).…”