LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

Abstract

Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a “domino days spreading” branching process in which successive amplifications may interact positively.

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

“…Nevertheless, these elements, such as Gypsy/Ty3-like elements (Metaviridae) or Copia/Ty1-like elements (Pseudoviridae), which are widely represented in invertebrates, fungi, and some protists, encode virion proteins (Fig. 6B) and form particles, thus meeting the definition of a virus (107)(108)(109).…”

Impacts of environmental and biological stressors on immune system of Macrobrachium rosenbergii

“…Recently, Piednoël et al . () reported LTR transposons from the shrimp Rimicaris exoculata . Thus, it is predicted that RT and IN could be common among crustaceans.…”

Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics

“…Copia and Gypsy elements are widely distributed among genomes of plants, fungi and animals but no BEL/Pao elements have been identified in plants, fungi or mammals so far [ 11 ] In metazoans, the three superfamilies display uneven relative abundances among genomes that greatly depend on both the element type and the host taxon considered. Previous comparative analyses in insects, nematodes and chordates [ 12 ], crustaceans [ 13 ], fungi [ 14 ] and more specifically Pezizomycotina [ 8 ], revealed that Gypsy and Copia elements display different distribution, representativeness and diversity. The Gypsy elements seem clearly the most abundant LTR-retrotransposon superfamily, found in almost all tested species, with a large number of copies in the available genomes.…”