Terminal-repeat retrotransposons in miniature (TRIMs) in bivalves

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 elementXunta de Galicia | Ref. ED431C 2016-037Xunta de Galicia | Ref. ED481B/2018/091Ministarstvo Znanosti, Obrazovanja i Sporta | Ref. 098-0982913-275

Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location

The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species.Versión del editor4,411

Chromosomal mapping of U1 snRNA genes to chromosomes of <i>Merluccius merluccius</i>.

<p>FISH experiments using a U1 snDNA probe (green) on chromosomes counterstained with PI (<b>a</b>) show signals on many chromosome pairs. The brightest signals appear on one pair (arrowheads in <b>a</b>) but there are also strong, consistent, signals (asterisks in <b>a</b>) on four more pairs. The corresponding karyotype shows that those signals are on chromosome pairs 13 and 5, 16, 17 and 19. Other signals are also clearly visible in many other pairs (<b>a</b>, <b>c</b>) but they are fainter and/or not always present in both homologues of each pair. FISH experiment on the same metaphase counterstained with DAPI (<b>b</b>, <b>c</b>) shows that 28S rDNA (green) and 5S rDNA (red) clusters are separated from the U1 snRNA gene clusters but that the single U2 snRNA gene cluster on chromosome 13 is coincident with the biggest U1 snRNA cluster. Scale bars, 5 μm.</p