Chendan Wei1, Zhenyi Wang1, Jianyu Wang1, Jia Teng1, Shaoqi Shen1, Qimeng Xiao1, Shoutong Bao1, Yishan Feng1, Yan Zhang1, Yuxian Li1, Sangrong Sun1, Yuanshuai Yue1, Chunyang Wu1, Yanli Wang1, Tianning Zhou1, Wenbo Xu1, Jigao Yu2,3, Li Wang4, Jinpeng Wang5,6,7. 1. School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. 2. University of Chinese Academy of Sciences, Beijing, 100049, China. 3. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China. 4. School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. wlsh219@126.com. 5. School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. wangjinpeng@ibcas.ac.cn. 6. University of Chinese Academy of Sciences, Beijing, 100049, China. wangjinpeng@ibcas.ac.cn. 7. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China. wangjinpeng@ibcas.ac.cn.
Abstract
BACKGROUND: 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. 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. RESULTS: Using 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. CONCLUSION: Duplicated 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.
BACKGROUND: 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 riceOryza 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. RESULTS: Using 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. CONCLUSION: Duplicated 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.
Authors: Joshua C Stein; Yeisoo Yu; Dario Copetti; Derrick J Zwickl; Li Zhang; Chengjun Zhang; Kapeel Chougule; Dongying Gao; Aiko Iwata; Jose Luis Goicoechea; Sharon Wei; Jun Wang; Yi Liao; Muhua Wang; Julie Jacquemin; Claude Becker; Dave Kudrna; Jianwei Zhang; Carlos E M Londono; Xiang Song; Seunghee Lee; Paul Sanchez; Andrea Zuccolo; Jetty S S Ammiraju; Jayson Talag; Ann Danowitz; Luis F Rivera; Andrea R Gschwend; Christos Noutsos; Cheng-Chieh Wu; Shu-Min Kao; Jhih-Wun Zeng; Fu-Jin Wei; Qiang Zhao; Qi Feng; Moaine El Baidouri; Marie-Christine Carpentier; Eric Lasserre; Richard Cooke; Daniel da Rosa Farias; Luciano Carlos da Maia; Railson S Dos Santos; Kevin G Nyberg; Kenneth L McNally; Ramil Mauleon; Nickolai Alexandrov; Jeremy Schmutz; Dave Flowers; Chuanzhu Fan; Detlef Weigel; Kshirod K Jena; Thomas Wicker; Mingsheng Chen; Bin Han; Robert Henry; Yue-Ie C Hsing; Nori Kurata; Antonio Costa de Oliveira; Olivier Panaud; Scott A Jackson; Carlos A Machado; Michael J Sanderson; Manyuan Long; Doreen Ware; Rod A Wing Journal: Nat Genet Date: 2018-01-22 Impact factor: 38.330
Authors: Jeanmaire Molina; Martin Sikora; Nandita Garud; Jonathan M Flowers; Samara Rubinstein; Andy Reynolds; Pu Huang; Scott Jackson; Barbara A Schaal; Carlos D Bustamante; Adam R Boyko; Michael D Purugganan Journal: Proc Natl Acad Sci U S A Date: 2011-05-02 Impact factor: 11.205
Authors: HyeRan Kim; Bonnie Hurwitz; Yeisoo Yu; Kristi Collura; Navdeep Gill; Phillip SanMiguel; James C Mullikin; Christopher Maher; William Nelson; Marina Wissotski; Michele Braidotti; David Kudrna; José Luis Goicoechea; Lincoln Stein; Doreen Ware; Scott A Jackson; Carol Soderlund; Rod A Wing Journal: Genome Biol Date: 2008-02-28 Impact factor: 13.583