Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves

Eva Šatović,Andrea Cedilak,Daniel García-Souto,Andrea Luchetti,Juan J Pasantes,Barbara Mantovani,Miroslav Plohl

doi:10.1038/s41598-019-56502-y

Abstract

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this element.

Highlights

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous Long Terminal Repeat (LTR) retrotransposons consisting of two terminal direct repeats surrounding a short internal domain
Initial “all-versus-all” blast search carried out within 194 genomic fragments of these species (96 belonging to Donax trunculus, 36 to Ruditapes philippinarum and 62 to R. decussatus) resulted in sequence groupings based on high-scoring segment pairs, suggesting the presence of highly similar nucleotide sequences dispersed throughout different genomic environments
This work is the first report of TRIM element in the class Bivalvia. biv-TRIM elements have been detected in 11 species belonging to subclasses Heterodonta and Pteriomorphia, while its presence could not be confirmed in 5 species, belonging to the same subclasses (Table 1)

Summary

Introduction

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. Terminal repeat retrotransposons in miniature (TRIMs) are small (less than 1000 bp) non-autonomous LTR retrotransposons They contain terminal direct repeats (TDRs) of 100–250 bp, equivalent to LTRs, flanking an internal domain which starts with a primer binding site (PBS), complementary to a tRNA, and ends with a polypurine tract (PPT)[6]. These elements were originally described in potato and Arabidopsis[6] and later found in many more plant genomes, from land plants to algae[7,8,9,10]. TRIM elements seem to be involved in active restructuring of plant genomes by affecting their promoters and coding regions They can be implicated in transduction of host genes or serve as hotspots for further retrotransposon insertions[6]. This is the first report of a TRIM in bivalve mollusks

Methods

Results

Conclusion