title: Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.
abstract: The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Yuantao
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Siqi
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Citrus Research Institute, Southwest University, Chongqing, P.R. China.
authors.forename: Li
authors.initials: L
authors.lastname: Cao
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Guizhi
authors.initials: G
authors.lastname: Wu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Chunli
authors.initials: C
authors.lastname: Chen
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Huiwen
authors.initials: H
authors.lastname: Yu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Yang
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Lan
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Lun
authors.initials: L
authors.lastname: Wang
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Jidi
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Zongzhou
authors.initials: Z
authors.lastname: Xie
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Meilian
authors.initials: M
authors.lastname: Tan
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Larkin
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Bin-Guang
authors.initials: BG
authors.lastname: Ma
authors.affiliation: College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China.|Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Xiuxin
authors.initials: X
authors.lastname: Deng
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P.R. China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Xu
mesh_terms: D060832:Apomixis / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D002957:Citrus / Q000145:classification / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012100:Reproduction, Asexual / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity