Identification of a genome-specific repetitive element in the Gossypium D genome

PeerJ

article

Hejun Lu¹  Xinglei Cui²  Yanyan Zhao²  Richard Odongo Magwanga²  Pengcheng Li²  Xiaoyan Cai²  Zhongli Zhou²  Xingxing Wang²  Yuling Liu⁴  Yanchao Xu²  Yuqing Hou²  Renhai Peng⁴  Kunbo Wang²  Fang Liu² 

[1]Gembloux Agro-Bio Tech, University of Liège

[2]Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science

[3]School of Biological and Physical Sciences ,(SBPS), Jaramogi Oginga Odinga University of Science and Technology

[4]Anyang Institute of Technology

[5]Tarium University

关键词: Gossypium;    Repetitive element;    D genome;    Fluorescence in situ hybridization (FISH);    Genome-specific;    Evolution;   

DOI  :  10.7717/peerj.8344

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY