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 Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon).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

Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi

“…To infer phylogenetic trees, amino acid sequence of INT,RH and RT from other known organisms were obtained from the GYDB database and recent studies [ 47 , 53 , 63 ], and aligned using MAFFT v7.407 [ 64 ] to amino acid sequence of INT, RT and RH from LTR retrotransposons found in L. luymesi genome. Each of the 3 domains was analyzed separately and a combined analysis was not done due to difference in taxon sampling and the fact that the domains may have distinct evolutionary histories.…”

Molecular cloning, expressional analyses and functional identification of TRAIL in tilapia, Oreochromis niloticus

“…qRT‐PCR was conducted with an ABI 7900HT real‐time PCR machine using a SYBR Green Real‐time PCR Master Mix (QPK‐201) kit (Toyobo). Amplification conditions were set up as follows: 95°C for 3 min, followed by 40 cycles of 95°C for 15 s, 55°C for 15 s and 72°C for 20 s. A serial dilution (10 −1 to 10 −6 fmol/μl) of plasmids containing the sequences of TNFSF10 and β‐actin was separately used to generate standard curve by plotting the logarithm of the plasmid copy number against the measured Ct values, which were used to quantify gene amplification rates for the of TNFSF10 or β‐actin (Cao et al., 2016). Data were normalized to β‐actin.…”