Tandem duplications of receptor-like kinase genes reshaped the homologous chromosome 1 regions in Oryza sativa ssp. indica and japonica and their possible ancestral genomes
Citation
Wang, Z., Guo, H., Cloutier, S. (2017). Tandem duplications of receptor-like kinase genes reshaped the homologous chromosome 1 regions in Oryza sativa ssp. indica and japonica and their possible ancestral genomes. Molecular Breeding, [online] 37(1), http://dx.doi.org/10.1007/s11032-016-0594-4
Plain language summary
Genomes in general and plant genomes specifically could be said to be plastic as opposed to fixed. This plasticity is an important driver of evolution because it results in the reshaping of chromosomal regions or entire chromosomes which, in turn, impact gene organization, mutation and expression. Several mechanisms contribute to this plasticity. Here, we performed an in-depth analysis of a region of rice chromosome 1 where several plant receptor-like kinase genes reside. We analyzed the DNA sequence of the equivalent region in the two cultivated species of rice and in two wild relative species. Through mechanisms of duplication in pairs, this region more than doubled in size in cultivated rice species resulting in a greater number of kinase genes, thereby creating new kinase genes that act as drivers of evolution.
Abstract
Plant receptor-like kinase (Rlk) genes form a large family, each encoding a protein with a signal motif, a single transmembrane region, and a cytoplasmic kinase domain. Various gene duplications have contributed to the establishment and expansion of the family. Here, we characterized the formation and evolution of the Rlk gene family in cultivated rice and their possible progenitors. Using wheat Rlk gene sequences, we identified orthologs from the genomes of domesticated rice subspecies Oryza sativa ssp. japonica and ssp. indica and their putative progenitors O. glaberrima and O. rufipogon. The four chromosome 1 orthologous regions ranged from 103 to 281 kb comprising 181 syntenic blocks with 75 to 100% sequence identity. These regions contained 11–19 Triticum aestivum kinases (Taks) and 10–15 Lr10 receptor-like kinases (Lrks) organized in clusters and 3–12 transposable elements (TEs). Dot plot analyses showed that the 4 regions had 21–37 conserved catalytic domains, mainly in protein kinases (PKs) and tyrosine kinases (TyrKs) in coupling state. Over 50% of the sequences of glaberrima/rufipogon and japonica/indica pairs were colinear, while japonica/indica displayed a marked sequence expansion with duplicated genes and TEs. A total of 2312 single nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) were identified between japonica and indica. Duplication of the Rlk genes in O. glaberrima and O. rufipogon occurred after the grass species radiation and before the divergence of O. rufipogon from O. glaberrima; the orthologous Rlk genes from O. japonica and O. indica duplicated after O. sativa separated from O. rufipogon; paralogs, obtained through extensive duplication, happened after the separation of rice from maize. Tandem duplication was the major factor contributing to the gene copy number variation and genome size expansion.