Dataset Information

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection.

ABSTRACT: BACKGROUND:Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~?50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited. RESULTS:Here, we explored gene expression divergence between a japonica rice cultivar Nipponbare and an indica rice cultivar 93-11 in response to invasion by the filamentous ascomycete fungus Magnaporthe oryzae (Pyricularia oryzae), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of cis-regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence. CONCLUSION:We proposed that variation in the expression patterns of these orthologous genes mediated by cis-regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to M. oryzae infection.

SUBMITTER: Zhong Z

PROVIDER: S-EPMC6397267 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection.

Zhong Zhenhui Z Lin Lianyu L Chen Meilian M Lin Lili L Chen Xiaofeng X Lin Yahong Y Chen Xi X Wang Zonghua Z Norvienyeku Justice J Zheng Huakun H

Rice (New York, N.Y.) 20190301 1

<h4>Background</h4>Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited.<h4 ...[more]

PMID: 30825020

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Project description: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.

Dataset Information

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection.

Publications

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection.

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