title: Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian.
abstract: A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Cao
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Yin
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
authors.forename: Zheming
authors.initials: Z
authors.lastname: Cao
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China. bingxw@ffrc.cn.
authors.forename: Xuwen
authors.initials: X
authors.lastname: Bing
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China. dingwd@126.com.
authors.forename: Weidong
authors.initials: W
authors.lastname: Ding
mesh_terms: D000818:Animals; D002347:Carps / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D018628:Gene Dosage; D015870:Gene Expression; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D016366:Open Reading Frames; D009928:Organ Specificity / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements; D020079:Terminal Repeat Sequences; D014158:Transcription, Genetic
chemical_list: D018626:Retroelements
keywords: Copy number; Cyprinus carpio var. Jian; Fluorescent in situ hybridization; Retrotransposon