Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence

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 similar to 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 similar to 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.

Automated summary

Duplicated genes in rice subspecies generated by ancient polyploidy around 100 million years ago are still being affected by gene conversion at a high frequency, impacting the divergence of rice subspecies. Ongoing gene conversion events maintain similarity between ancient duplicates, accelerate rice divergence, and affect biological functions associated with multiple genes. The converted genes tend to have more similar expression patterns than nonconverted duplicates, suggesting interaction opportunities among members of large gene families.