PMID- 27006694 OWN - NLM STAT- PubMed-not-MEDLINE DCOM- 20160323 LR - 20201001 IS - 1755-8166 (Print) IS - 1755-8166 (Electronic) IS - 1755-8166 (Linking) VI - 9 DP - 2016 TI - A Gossypium BAC clone contains key repeat components distinguishing sub-genome of allotetraploidy cottons. PG - 27 LID - 10.1186/s13039-016-0235-y [doi] LID - 27 AB - BACKGROUND: Dissecting genome organization is indispensable for further functional and applied studies. As genome sequences data shown, cotton genomes contain more than 60 % repetitive sequences, so study on repetitive sequences composition, structure, and distribution is the key step to dissect cotton genome. RESULTS: In this study, a bacterial artificial chromosome (BAC) clone enriched in repetitive sequences, was discovered initiatively by fluorescence in situ hybridization (FISH). FISHing with allotetraploidy cotton as target DNA, dispersed signals on most regions of all A sub-genome chromosomes, and only middle regions of all D sub-genome chromosomes were detected. Further FISHing with other cotton species bearing A or D genome as target DNA, specific signals were viewed. After BAC sequencing and bioinformational analysis, 129 repeat elements, size about 57,172 bp were found, accounting for more than 62 % of the BAC sequence (91,238 bp). Among them, a type of long terminal repeat-retrotransposon (LTR-RT), LTR/Gypsy was the key element causing the specific FISH results. Using the fragments of BAC matching with the identified Gypsy-like LTR as probes, the BAC-57I23-like FISH signals were reappeared. Running BLASTN, the fragments had good match with all chromosomes of G. arboreum (A2) genome and A sub-genome of G. hirsutum (AD1), and had relatively inferior match with all chromosomes of D sub-genome of AD1, but had little match with the chromosomes of G. raimondii (D5) genome, which was consistent with the FISH results. CONCLUSION: A repeats-enriched cytogenetic marker to identify A and D sub-genomes of Gossypium was discovered by FISH. Combined sequences analysis with FISH verification, the assembly quality of repetitive sequences in the allotetraploidy cotton draft genome was assessed, and better chromosome belonging was verified. We also found the genomic distribution of the identified Gypsy-LTR-RT was similar to the distribution of heterochromatin. The expansion of this type of Gypsy-LTR-RT in heterochromatic regions may be one of the major reasons for the size gap between A and D genome. The findings showed here will help to understand the composition, structure, and evolution of cotton genome, and contribute to the further perfection of the draft genomes of cotton. FAU - Liu, Yuling AU - Liu Y AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China. FAU - Peng, Renhai AU - Peng R AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; Anyang Institute of Technology, Anyang, Henan 455000 China. FAU - Liu, Fang AU - Liu F AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Wang, Xingxing AU - Wang X AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Cui, Xinglei AU - Cui X AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Zhou, Zhongli AU - Zhou Z AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Wang, Chunying AU - Wang C AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Cai, Xiaoyan AU - Cai X AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Wang, Yuhong AU - Wang Y AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. FAU - Lin, Zhongxu AU - Lin Z AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China. FAU - Wang, Kunbo AU - Wang K AD - State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China. LA - eng PT - Journal Article DEP - 20160322 PL - England TA - Mol Cytogenet JT - Molecular cytogenetics JID - 101317942 PMC - PMC4802715 OTO - NOTNLM OT - BAC OT - FISH OT - Gossypium OT - LTR-RT OT - Repetitive sequences EDAT- 2016/03/24 06:00 MHDA- 2016/03/24 06:01 PMCR- 2016/03/22 CRDT- 2016/03/24 06:00 PHST- 2016/02/18 00:00 [received] PHST- 2016/03/14 00:00 [accepted] PHST- 2016/03/24 06:00 [entrez] PHST- 2016/03/24 06:00 [pubmed] PHST- 2016/03/24 06:01 [medline] PHST- 2016/03/22 00:00 [pmc-release] AID - 235 [pii] AID - 10.1186/s13039-016-0235-y [doi] PST - epublish SO - Mol Cytogenet. 2016 Mar 22;9:27. doi: 10.1186/s13039-016-0235-y. eCollection 2016.