Abstract
BackgroundDuplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution.ResultsUsing comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19–5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77–9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion.ConclusionDuplicated genes in rice subspecies generated by grass polyploidization ~ 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.
Highlights
Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes
Using these inferred collinear genes of the three rice genomes, we identified duplicated genes produced by the whole-genome duplication (WGD) common to the grasses at ~ 100 mya, according to the sequence similarity of collinear gene pairs and our previous identification of WGD event-related homologous chromosome regions [62]
We found that the expression difference of converted gene pairs was significantly lower than that of nonconverted gene pairs in the three rice genomes
Summary
Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. Asian rice is planted worldwide, feeding half of the world’s population as a staple food and providing more than 20% of the energy for human survival [2,3,4].Oryza sativa ssp. The whole-genome sequence of XI (93–11) has been published [8], and high-quality genome sequences of representative varieties Zhenshan 97 (XI-ZS97) and Minghui 63 (XI-MH63) have been made available [9]. These two main varieties of XI (XIZS97 and XI-MH63) are the parents of an excellent Chinese hybrid. XI accounts for more than 70% of global rice production and possesses much higher genetic diversity than GJ [10], as highlighted by a recent analysis of 3010 diverse Asian cultivated rice genomes and 1275 rice varieties with resequenced genomes [4, 11]
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