Molecular Evolution of Receptor-Like Kinase Genes in Hexaploid Wheat. Independent Evolution of Orthologs after Polyploidization and Mechanisms of Local Rearrangements at Paralogous Loci

Abstract

Hexaploid wheat is a young polyploid species and represents a good model to study mechanisms of gene evolution after polyploidization. Recent studies at the scale of the whole genome have suggested rapid genomic changes after polyploidization but so far the rearrangements that have occurred in terms of gene content and organization have not been analyzed at the microlevel in wheat. Here, we have isolated members of a receptor kinase (Lrk) gene family in hexaploid and diploid wheat, Aegilops tauschii, and barley (Hordeum vulgare). Phylogenetic analysis has allowed us to establish evolutionary relationships (orthology versus paralogy) between the different members of this gene family in wheat as well as with Lrk genes from barley. It also demonstrated that the sequences of the homoeologous Lrk genes evolved independently after polyploidization. In addition, we found evidence for gene loss during the evolution of wheat and barley. Analysis of large genomic fragments isolated from nonorthologous Lrk loci showed a high conservation of the gene content and gene organization at these loci on the homoeologous group 1 chromosomes of wheat and barley. Finally, sequence comparison of two paralogous fragments of chromosome 1B showed a large number of local events (sequence duplications, deletions, and insertions), which reveal rearrangements and mechanisms for genome enlargement at the microlevel.

Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat[W]

“…In maize and wheat, genes were found to be organized in gene islands or as single genes separated by large regions of nested repetitive elements (reviewed by Feuillet and Keller, 2002). In addition to expressed genes, gene fragments have been found in several sequenced regions in grass genomes (Feuillet and Keller, 1999;Feuillet et al, 2001;Ramakrishna et al, 2002b). Illegitimate recombination and double-strand break repair mechanisms that introduce filler sequences into chromosomes might be responsible for genome restructuring and the formation of truncated genes (Ramakrishna et al, 2002b).…”

Sequence-Level Analysis of the Diploidization Process in the TriplicatedFLOWERING LOCUS CRegion ofBrassica rapa

“…The long-term evolution of polyploid genomes is generally a diploidization process occurring through an extensive genome reorganization at both the gene and chromosome levels (Cronn et al, 1999;Wendel, 2000;Feuillet et al, 2001;Lysak et al, 2005). In the genome of Arabidopsis thaliana, which contains ;29,000 genes, increases in the sizes of gene families have occurred partly via three rounds of apparent whole genome duplication (1R, 2R, and 3R at ;350 to 300, ;170 to 156, and ;26.7 to 25.0 million years ago [MYA], respectively) and via gradual accumulation of small-scale gene/ segmental duplications during the last ;350 million years (Bowers et al, 2003;Maere et al, 2005).…”

Single Mutations Silence Pgic2 Genes in Two Very Recent Allotetraploid Species of Clarkia

“…But these genes were not examined over their entire lengths, nor was their expression studied. Sequence analysis of a small family of receptor-like kinase genes in hexaploid wheat showed independent evolution of homoeologous genes and identified several sequences with stop codons, suggesting they are not expressed (Feuillet et al 2001). PgiC genes in allotetraploid Clarkia gracilis were found to be evolving at similar rates to their orthologues in related diploid species, and there was no evidence of silencing (Ford and Gottlieb 1999).…”