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Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd.
Gene. 2014 Nov 01; 551(1):26-32.GENE

Abstract

Wax gourd (2n=2x=24) is an important vegetable species in Cucurbitaceae. Because it can be stored for a very long period of time, it plays an important role in ensuring the annual supply and regulating off-season supply of the vegetables. However, the availability of genetic information about wax gourd is limited. This study aimed to identify the useful genetic information for wax gourd. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia retrotransposons were isolated from the genome of wax gourd using degenerate oligonucleotide primers. A total of twenty eight RT sequences were obtained, which showed high heterogeneity with the similarity ranging from 47.5% to 94.3%. Sixteen (57.1%) of them were found to be defective, being disrupted by stop codons and/or frameshift mutations. These 28 sequences were divided into five subfamilies. The comparative phylogenetic analysis with other Cucurbitaceae species from GenBank database showed that most retrotransposons derived from the same genus tended to cluster together, although there were a few exceptions. These results indicate that both vertical transmission and horizontal transmission are the sources of Ty1-copia retrotransposons in wax gourd. Fluorescent in situ hybridization (FISH) with Ty1-copia retrotransposon sequences as probes revealed that this kind of retrotransposons had a dispersed genomic organization, physically distributed among all the chromosomes of wax gourd, with clusters in the heterochromatin regions. This is the first report of Ty1-copia retrotransposons in wax gourd, which would be helpful for our understanding about the organization and evolutions of wax gourd genome and also provide valuable information for our utilization of wax gourd retrotransposons.

Authors+Show Affiliations

Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China.Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China. Electronic address: dasenxie@21cn.com.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25108132

Citation

Jiang, Biao, et al. "Characterization and Chromosomal Organization of Ty1-copia Retrotransposons in Wax Gourd." Gene, vol. 551, no. 1, 2014, pp. 26-32.
Jiang B, Liu W, Peng Q, et al. Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd. Gene. 2014;551(1):26-32.
Jiang, B., Liu, W., Peng, Q., He, X., & Xie, D. (2014). Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd. Gene, 551(1), 26-32. https://doi.org/10.1016/j.gene.2014.08.014
Jiang B, et al. Characterization and Chromosomal Organization of Ty1-copia Retrotransposons in Wax Gourd. Gene. 2014 Nov 1;551(1):26-32. PubMed PMID: 25108132.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd. AU - Jiang,Biao, AU - Liu,Wenrui, AU - Peng,Qingwu, AU - He,Xiaoming, AU - Xie,Dasen, Y1 - 2014/08/07/ PY - 2013/09/26/received PY - 2014/06/09/revised PY - 2014/08/05/accepted PY - 2014/8/10/entrez PY - 2014/8/12/pubmed PY - 2015/7/15/medline KW - FISH KW - Heterogeneity KW - Reverse transcriptase KW - Ty1-copia retrotransposons KW - Wax gourd SP - 26 EP - 32 JF - Gene JO - Gene VL - 551 IS - 1 N2 - Wax gourd (2n=2x=24) is an important vegetable species in Cucurbitaceae. Because it can be stored for a very long period of time, it plays an important role in ensuring the annual supply and regulating off-season supply of the vegetables. However, the availability of genetic information about wax gourd is limited. This study aimed to identify the useful genetic information for wax gourd. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia retrotransposons were isolated from the genome of wax gourd using degenerate oligonucleotide primers. A total of twenty eight RT sequences were obtained, which showed high heterogeneity with the similarity ranging from 47.5% to 94.3%. Sixteen (57.1%) of them were found to be defective, being disrupted by stop codons and/or frameshift mutations. These 28 sequences were divided into five subfamilies. The comparative phylogenetic analysis with other Cucurbitaceae species from GenBank database showed that most retrotransposons derived from the same genus tended to cluster together, although there were a few exceptions. These results indicate that both vertical transmission and horizontal transmission are the sources of Ty1-copia retrotransposons in wax gourd. Fluorescent in situ hybridization (FISH) with Ty1-copia retrotransposon sequences as probes revealed that this kind of retrotransposons had a dispersed genomic organization, physically distributed among all the chromosomes of wax gourd, with clusters in the heterochromatin regions. This is the first report of Ty1-copia retrotransposons in wax gourd, which would be helpful for our understanding about the organization and evolutions of wax gourd genome and also provide valuable information for our utilization of wax gourd retrotransposons. SN - 1879-0038 UR - https://www.unboundmedicine.com/medline/citation/25108132/Characterization_and_chromosomal_organization_of_Ty1_copia_retrotransposons_in_wax_gourd_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0378-1119(14)00927-5 DB - PRIME DP - Unbound Medicine ER -