Identification of a genome-specific repetitive element in the Gossypium D genome
Hejun Lu,
Xinglei Cui,
Yanyan Zhao,
Richard Odongo Magwanga,
Pengcheng Li,
Xiaoyan Cai,
Zhongli Zhou,
Xingxing Wang,
Yuling Liu,
Yanchao Xu,
Yuqing Hou,
Renhai Peng,
Kunbo Wang,
Fang Liu
Affiliations
Hejun Lu
Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium
Xinglei Cui
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Yanyan Zhao
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Richard Odongo Magwanga
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Pengcheng Li
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Xiaoyan Cai
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Zhongli Zhou
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Xingxing Wang
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Yuling Liu
Anyang Institute of Technology, Anyang, Henan, China
Yanchao Xu
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Yuqing Hou
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Renhai Peng
Anyang Institute of Technology, Anyang, Henan, China
Kunbo Wang
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
Fang Liu
Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
