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

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

Background

Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid.

Results

We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity.

Conclusions

Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07749-1.

Characterization of a novel brain cell line from Jian carp (Cyprinus carpio var. Jian)

Jian carp (Cyprinus carpio var. Jian) is an economically important cultured fish in China. Currently, it is facing threats from infectious diseases including koi herpesvirus (KHV). Here, we established a new cell line, designated CCB-J, derived from the brain tissue of the Jian carp. CCB-J cells grew well in Leibovitz's L-15 medium containing 20% fetal bovine serum at 25 °C and have been subcultured for more than 60 passages. At the 30th passage, analysis showed that the number of chromosomes was 100, which is identical to that of other carp variants. Sequencing of the 18S ribosomal DNA confirmed that CCB-J originated from Jian carp. After transfection with the pEGFP-N1 plasmid, green fluorescence was observed in CCB-J. The replication of KHV in CCB-J cells was confirmed by RT-PCR and transmission electron microscopy. The viral titers of KHV in CCB-J cells and CCB cells, which have been widely used in the study of KHV, reached 10^3.9 and 10^1.8 median tissue culture infectious dose (TCID₅₀/mL), respectively, within 14 days. The result of TaqMan PCR revealed that CCB-J cells were more sensitive to KHV than CCB cells. Meanwhile, a cytopathic effect (CPE) was also observed in the CCB-J cells in a shorter time post-infection compared with CCB cells. In summary, the CCB-J cell line will be a useful tool in the study of viral pathogenesis and vaccine research.