PMID- 31915591
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20200930
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 8
DP  - 2020
TI  - Identification of a genome-specific repetitive element in the Gossypium D genome.
PG  - e8344
LID - 10.7717/peerj.8344 [doi]
LID - e8344
AB  - 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 (D(5)) genome but rarely in the 
      diploid Gossypium arboreum (A(2)) 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 D(5) and D-subgenomes but not in the A(2) 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 D(5)genome. 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.
CI  - (c)2020 Lu et al.
FAU - Lu, Hejun
AU  - Lu H
AD  - Gembloux Agro-Bio Tech, University of Liege, Gembloux, Namur, Belgium.
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Cui, Xinglei
AU  - Cui X
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Zhao, Yanyan
AU  - Zhao Y
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Magwanga, Richard Odongo
AU  - Magwanga RO
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
AD  - School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga 
      University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya.
FAU - Li, Pengcheng
AU  - Li P
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Cai, Xiaoyan
AU  - Cai X
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Zhou, Zhongli
AU  - Zhou Z
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Wang, Xingxing
AU  - Wang X
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Liu, Yuling
AU  - Liu Y
AD  - Anyang Institute of Technology, Anyang, Henan, China.
FAU - Xu, Yanchao
AU  - Xu Y
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Hou, Yuqing
AU  - Hou Y
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
FAU - Peng, Renhai
AU  - Peng R
AD  - Anyang Institute of Technology, Anyang, Henan, China.
FAU - Wang, Kunbo
AU  - Wang K
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
AD  - Tarium University, Alar, Xinjiang, China.
FAU - Liu, Fang
AU  - Liu F
AD  - Research Base of Tarium University, State Key Laboratory of Cotton Biology, 
      Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 
      Henan, China.
LA  - eng
PT  - Journal Article
DEP - 20200103
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
PMC - PMC6944119
OTO - NOTNLM
OT  - D genome
OT  - Evolution
OT  - Fluorescence in situ hybridization (FISH)
OT  - Genome-specific
OT  - Gossypium
OT  - Repetitive element
COIS- The authors declare there are no competing interests.
EDAT- 2020/01/10 06:00
MHDA- 2020/01/10 06:01
PMCR- 2020/01/03
CRDT- 2020/01/10 06:00
PHST- 2019/06/14 00:00 [received]
PHST- 2019/12/04 00:00 [accepted]
PHST- 2020/01/10 06:00 [entrez]
PHST- 2020/01/10 06:00 [pubmed]
PHST- 2020/01/10 06:01 [medline]
PHST- 2020/01/03 00:00 [pmc-release]
AID - 8344 [pii]
AID - 10.7717/peerj.8344 [doi]
PST - epublish
SO  - PeerJ. 2020 Jan 3;8:e8344. doi: 10.7717/peerj.8344. eCollection 2020.