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Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian

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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 Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon).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.

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Abbreviations

LTR:

Long terminal repeat

ORF:

Open reading frame

GAG:

Group-specific antigen

POL:

Polyprotein

PR:

Protease

RT:

Reverse transriptase

RH:

RNase H

IN:

Integrase

IR:

Inverted repeat

PBS:

Primer binding site

PPT:

Polypurine tract

UGW:

Universal Genome Walker™

AFLP:

Amplified fragment length polymorphism

NJ:

Neighbor-joining

RT-PCR:

Reverse transcriptase-polymerase chain reaction

PTGS:

Post-transcriptional gene silencing

JRE:

Cyprinus carpio var. Jian retrotransposon

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Acknowledgments

This research was supported by the National Natural Science Foundation of China (31200918), and the Natural Science Foundation of Jiangsu Province (BK2011184).

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Authors and Affiliations

  1. Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China

    Liping Cao, Guojun Yin, Zheming Cao, Xuwen Bing & Weidong Ding

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  1. Liping Cao
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  2. Guojun Yin
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  3. Zheming Cao
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  5. Weidong Ding
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Correspondence to Xuwen Bing or Weidong Ding.

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Cao, L., Yin, G., Cao, Z. et al. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian. Genetica 144, 325–333 (2016). https://doi.org/10.1007/s10709-016-9901-6

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