Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

Abstract

The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.

The genome of the domesticated apple (Malus × domestica Borkh.)

“…3). The rate of chromosome rearrangements after polyploidization (12 chromosome events in 60 My) is similar to that for poplar (~16 events in 60 My) 6 and lower than in maize (at least 17 chromosome fusion events in 5 My) 33 or in artificial neopolyploids 34 . In this sense, molecular clocks of perennial woody species seem slower than those of annual species, in terms of both nucleotide substitutions and chromosome rearrangements 9 .…”

The ZmASR1 Protein Influences Branched-Chain Amino Acid Biosynthesis and Maintains Kernel Yield in Maize under Water-Limited Conditions

“…Phylogenetic analyses indicated several duplication events after the divergence of Liliales from Commelinids, giving rise to five paralogous clades of ASR genes in the Poaceae family. Anchoring of the ASR genes on the maize physical map shows that all Poaceae sequences can be assigned to one of the Poaceae ancestor protochromosomes previously defined by Salse et al (2008). Thus, sequences from the subclades I-1, I-2, I-3, II-1, and II-2 trace back to chromosomes A11/A12, A4, A1, A2/A4, and A1, respectively.…”

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

“…Multiple WGDs and subsequent chromosome number reduction resulting in a mosaic of parental genomic blocks are well documented in grasses (Salse et al, 2008;Luo et al, 2009) and in the allopolyploid B. napus (Lysak et al, 2005;Parkin et al, 2005;.…”