GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species

Abstract

Crustacean species have not been examined in great detail for their transposable elements content. Here we focus on galatheid crabs, which are one of the most diverse and widespread taxonomic groups of Decapoda. Ty1/copia retrotransposons are a diverse and taxonomically dispersed group. Using degenerate primers, we isolated several DNA fragments that show homology with Ty1/copia retroelements reverse transcriptase gene. We named the corresponding elements from which they originated GalEa1 to GalEa3 and analyzed one of them further by isolating various clones containing segments of GalEa1. This is the first LTR retrotransposon described in crustacean genome. Nucleotide sequencing of the clones revealed that GalEa1 has LTRs (124 bp) and that the internal sequence (4,421 bp) includes a single large ORF containing gag and pol regions. Further screening identified highly related elements in six of the nine galatheid species studied. By performing BLAST searches on genome databases, we could also identify GalEa-like elements in some fishes and Urochordata genomes. These elements define a new clade of Ty1/copia retrotransposons that differs from all other Ty1/copia elements and that seems to be restricted to aquatic species.

Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi

“…The length of the fungal GalEa retrotransposons ranges from 5428 bp (Oima1 from O. maius ) to 7018 bp (Cogra2 from C. graminicola ), with an average length of 6100 bp. They appear thus larger than the GalEa elements previously described in metazoans (up to 4949 bp for CoRex1 [24]). They are however very similar to the other GalEa with : (i) LTRs bordered by 5’-TGT and 3’-CA with an average size of 235 bp (from 138 to 311 bp, excluding the outlier Cormil element that has 545 bp LTRs); (ii) a 5 bp Target Site Duplication as observed for Zeco1 in D. rerio ; (iii) a large single ORF; and (iv) a great variability in the PolyPurine Tract signal.…”

“…The branch 2 groups at least 13 widely distributed clades among eukaryotes, while the branch 1 comprises Ty (Pseudovirus) elements found in fungi together with four clades of CoDi-like elements from diatoms and the GalEa clade. Initially described in galatheids (Galatheid Euminida a nnulosa [24]), GalEa elements have been actually more successful among metazoan species than initially thought with some elements identified in Mollusca, Chordata, Cnidaria, Ctenophora, Echinoderma and Hemichordata [15]. Numerous GalEa sequences have been also identified from some microbial metagenomes collected during the Sargasso Sea surveys [25].…”

Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis

“…At present, however, LTR sequences have not been identified in PyRE10G, whereas most GalEa group elements possess LTR sequences at both ends. Considering the distribution of GalEa elements among phylogenetically distant aquatic animals, Terrat et al (2008) speculated horizontal gene transfer as one reason for the unusual distribution. The present data raise the possibility that GalEa group elements exist in plants.…”

“…In the tree, PyRE1G1 was grouped in the clade of usual copia retrotransposons while PyRE10G was in another clade of the GalEa group. Most recently, Terrat et al reported that GalEa elements isolated from galatheid crabs are closely related to copia-like elements in phylogenetically distant animals such as Ciona intestinalis, Oryzias latipes, and Danio rerio and concluded that the GalEa group is a new clade of copia-like retrotransposons in aquatic animals (Terrat et al, 2008). The inclusion of PyRE10G in the clade of GalEa elements (Fig.…”

“…Most recently, we found that PyRE10G is closely related to a new clade of copia retrotransposons distributed only among aquatic animals (Terrat et al, 2008). The gene structure of PyRE1G1 was also compared with that of PyRE10G.…”