title: Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants.
abstract: Hibiscus syriacus (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the H. syriacus genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of H. syriacus, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including H. syriacus, Arabidopsis thaliana, Gossypium raimondii, Theobroma cacao and Amborella trichopoda. We inferred their evolutionary relationships based on divergence times among Malvaceae plant genes and found that gene families involved in flowering regulation and disease resistance were more highly divergent and expanded in H. syriacus than in its close relatives, G. raimondii (DD) and T. cacao. Clustered gene families and gene collinearity analysis revealed that two recent rounds of whole-genome duplication were followed by diploidization of the H. syriacus genome after speciation. Copy number variation and phylogenetic divergence indicates that WGDs and subsequent diploidization led to unequal duplication and deletion of flowering-related genes in H. syriacus and may affect its unique floral morphology.
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Kim
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Seungill
authors.initials: S
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Namjin
authors.initials: N
authors.lastname: Koo
authors.affiliation: Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
authors.forename: Ah-Young
authors.initials: AY
authors.lastname: Shin
authors.affiliation: Department of Agricultural Plant Science, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.
authors.forename: Seon-In
authors.initials: SI
authors.lastname: Yeom
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Eunyoung
authors.initials: E
authors.lastname: Seo
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Seong-Jin
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Department of Agricultural Plant Science, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.
authors.forename: Won-Hee
authors.initials: WH
authors.lastname: Kang
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Myung-Shin
authors.initials: MS
authors.lastname: Kim
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Jieun
authors.initials: J
authors.lastname: Park
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Insu
authors.initials: I
authors.lastname: Jang
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Pan-Gyu
authors.initials: PG
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Iksu
authors.initials: I
authors.lastname: Byeon
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Min-Seo
authors.initials: MS
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: JinHyuk
authors.initials: J
authors.lastname: Choi
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Gunhwan
authors.initials: G
authors.lastname: Ko
authors.affiliation: National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54875, Korea.
authors.forename: JiHye
authors.initials: J
authors.lastname: Hwang
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.affiliation: Division of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea.
authors.forename: Sang-Bong
authors.initials: SB
authors.lastname: Choi
authors.affiliation: Department of Horticultural Science, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea.
authors.forename: Je Min
authors.initials: JM
authors.lastname: Lee
authors.affiliation: Department of Horticultural Science, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea.
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.affiliation: Green Plant Institute, Yongin 446-908, Korea.
authors.forename: Jungho
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea.
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.affiliation: National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54875, Korea.
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.affiliation: Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
authors.forename: Suk-Yoon
authors.initials: SY
authors.lastname: Kwon
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Kim
mesh_terms: D004268:DNA-Binding Proteins / Q000235:genetics; D035264:Flowers / Q000254:growth & development*; D018745:Genome, Plant; D031584:Hibiscus / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family; D011123:Polyploidy; D016601:RNA-Binding Proteins / Q000235:genetics; D059467:Transcriptome
chemical_list: D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins
keywords: Diploidization; Hibiscus syriacus; Homeolog; Multivoltinism; Whole Genome Duplication