title: Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton.
abstract: Centromeric chromatin in most eukaryotes is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species. The evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. To obtain insight into the evolution of centromeric repeats following polyploidy, we studied a model diploid progenitor (Gossypium raimondii, D-genome) of the allopolyploid (AD-genome) cottons, G. hirsutum and G. barbadense. Sequence analysis of chromatin-immunoprecipitated DNA showed that the G. raimondii centromeric repeats originated from retrotransposon-related sequences. Comparative analysis showed that nine of the 10 analyzed centromeric repeats were absent from the centromeres in the A-genome and related diploid species (B-, F- and G-genomes), indicating that they colonized the centromeres of D-genome lineage after the divergence of the A- and D- ancestral species or that they were ancestrally retained prior to the origin of Gossypium. Notably, six of the nine repeats were present in both the A- and D-subgenomes in tetraploid G. hirsutum, and increased in abundance in both subgenomes. This finding suggests that centromeric repeats may spread and proliferate between genomes subsequent to polyploidization. Two repeats, Gr334 and Gr359 occurred in both the centromeres and nucleolar organizer regions (NORs) in D- and AD-genome species, yet localized to just the NORs in A-, B-, F-, and G-genome species. Contained within is a story of an established centromeric repeat that is eliminated and allopolyploidization provides an opportunity for reinvasion and reestablishment, which broadens our evolutionary understanding behind the cycles of centromeric repeat establishment and targeting.
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Jinlei
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Rick E
authors.initials: RE
authors.lastname: Masonbrink
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Shan
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Fengqin
authors.initials: F
authors.lastname: Song
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, China.
authors.forename: Weichang
authors.initials: W
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Kunbo
authors.initials: K
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D002503:Centromere / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism*; D011123:Polyploidy; D018626:Retroelements / Q000235:genetics*
chemical_list: D018626:Retroelements
keywords: 
  Gossypium raimondii
  ; centromere evolution; centromeric retrotransposon; dual targeting retrotransposon; rapid proliferation