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

, , , , , , , , , , , , ,
1 Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
2 Gembloux Agro-bio Tech, University of Liège, Gembloux, Namur, Belgium
3 School of biological and physical sciences,, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box, Bondo-Kenya
4 Anyang Istitute of Technology, Anyang, Henan, China
5 Tarium University, Alar, Xinjiang, China
DOI
10.7287/peerj.preprints.27806v1
Published
Accepted
Subject Areas
Agricultural Science, Evolutionary Studies, Genetics, Genomics, Plant Science
Keywords
Gossypium, Repetitive element, D genome, Fluorescence in situ hybridization (FISH), Genome-specific, Evolution
Copyright
© 2019 Lu et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Lu H, Cui X, Zhao Y, Magwang RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. 2019. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ Preprints 7:e27806v1

Abstract

The activity of genome-specific repetitive sequence is the main cause of the genome variation between Gossypium A and D genomes. Through the comparative analysis of the two genomes, we got a repetitive element (ICRd motif), which repeats massively in the diploid Gossypium raimondii (D5) genome while almost absent in the diploid Gossypium arboreum (A2) genome. We further explored the existence of ICRd motif in G. raimondii, G. arboreum, and two tetraploids (AADD) cotton G. hirsutum and G. barbadense by fluorescence in situ hybridization (FISH), and observed the ICRd motif exists in D5 and D-subgenomes but not in A2 and A-subgenome. The ICRd motif was investigated through its two constituents , a length variable tandem repeat region (TR) and a conservative sequence (CS), which highly repeat and evenly distribute in chromosomes of D5 genome. The ICRd motif was revealed as the common conservative region of ancient LTR-TEs. The identifications and investigation of the ICRd motif promote the study on the A and D genome differences, facilitate the research on the Gossypium genome evolution, and provide assistance to subgenome identification and genome assembling.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Blast of the 1.8 kb sequences in G. raimondi genome

DOI: 10.7287/peerj.preprints.27806v1/supp-1

The location of the ICRd motifs and their constituents in genome

DOI: 10.7287/peerj.preprints.27806v1/supp-2

The structures of the LTR-TEs harboring the ICRd motif

DOI: 10.7287/peerj.preprints.27806v1/supp-3

The information of the two homologous segments

DOI: 10.7287/peerj.preprints.27806v1/supp-4

Blast results of the ICRd motif with tetraploid cotton

DOI: 10.7287/peerj.preprints.27806v1/supp-5

The whole alignment of the 72 LTR-TEs

DOI: 10.7287/peerj.preprints.27806v1/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Hejun Lu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Xinglei Cui conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Yanyan Zhao performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Richard Odongo Magwang performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, data analysis and interperetation.

Pengcheng Li performed the experiments, contributed reagents/materials/analysis tools, approved the final draft, data collection.

Xiaoyan Cai performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Zhongli Zhou performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Xingxing Wang performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Yuling Liu performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Yanchao Xu performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Yuqing Hou performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Renhai Peng performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Kunbo Wang conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Fang Liu conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

The genome assemblies involved in this work of G. raimondii, G. arboreum, G. hirsutum are respectively downloaded from Cottongen and are available at :

https://www.cottongen.org/species/Gossypium_raimondii/jgi_genome_221

https://www.cottongen.org/species/Gossypium_arboreum/bgi-A2_genome_v2.0

https://www.cottongen.org/species/Gossypium_hirsutum/bgi-AD1_genome_v1.0

https://www.cottongen.org/species/Gossypium_hirsutum/nbi-AD1_genome_v1.1

https://www.cottongen.org/species/Gossypium_hirsutum/jgi-AD1_genome_v1.1

https://www.cottongen.org/species/Gossypium_barbadense/HAU-AD2_genome_v2.0

The other G. barbadense genome assembly is available in GenBank under PRJNA251673.

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.

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