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

doi:10.7717/peerj.8344

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

PeerJ. 2020 Jan 3:8:e8344. doi: 10.7717/peerj.8344. eCollection 2020.

Authors

Hejun Lu^#^{1

2}, Xinglei Cui^#², Yanyan Zhao², Richard Odongo Magwanga^{2

3}, Pengcheng Li², Xiaoyan Cai², Zhongli Zhou², Xingxing Wang², Yuling Liu⁴, Yanchao Xu², Yuqing Hou², Renhai Peng⁴, Kunbo Wang^{2

5}, Fang Liu²

Affiliations

¹ Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium.
² Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
³ School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya.
⁴ Anyang Institute of Technology, Anyang, Henan, China.
⁵ Tarium University, Alar, Xinjiang, China.

^# Contributed equally.

Abstract

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.

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

Grants and funding

This research was supported by the National Key Research and Development Plan of China (grants 2016YFD0100306 and 2016YFD0100203) and The Natural Science Foundation of China (grants 31530053 and 31671745). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.