Mobile Elements in Ray-Finned Fish Genomes

Abstract

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

“…This flattened appearance can be ascribed to the exceptionally large size of chromosomes (88.37–350.1 Mb) that are even larger than mammalian chromosomes (gorilla 32.72–219.76 Mb). More fluctuating GC% values exist in tetraodontid fish with reduced genome size ( Tetraodon nigroviridis , Takifugu rubripes , Figure 2 ; [ 41 , 42 , 43 ]) and to some extent in other species with reduced genomes e.g., the three-spined stickleback ( Gasterosteus aculeatus ). A combination of a flattened range of GC% values in large(r) chromosomes (i.e., macrochromosomes) and more or less clear GC% elevations in smaller chromosomes (i.e., microchromosomes) exists in the sterlet ( Acipenser ruthenus , Figure 2 j) and all three chondrichthyan species analysed ( Amblyraja radiata , Chiloscyllium plagiosum , and Pristis pectinata ).…”

“…More fluctuating GC% values exist in tetraodontid fish with reduced genome size ( Tetraodon nigroviridis , Takifugu rubripes , Figure 2 ; [ 41 , 42 , 43 ]) and to some extent in other species with reduced genomes e.g., the three-spined stickleback ( Gasterosteus aculeatus ).…”

Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

“…In chromosome 2 D. rerio revealed two major bursts of activity with ancient copies predominant but fewer recent copies ( Figure S19 ). In teleosts as a whole, significant interspecific differences in TE divergence have been observed [ 43 ], generally with one or two bursts of transposition [ 5 , 8 ]. Teleost genomes generally contain fewer ancient copies (K-values >25) than the genomes of other organisms such as mammals, suggesting differences in the process of elimination [ 8 ].…”

Transposable Elements and Teleost Migratory Behaviour

“…The genome size of ray-finned fish is characterised by a wide range of variation, with the smallest values found in Tetraodontiformes species (~0.35 Gb) and the highest values in Acipenseriformes (~9.5 Gb). These differences are mostly ascribable to the presence of repetitive DNA [ 6 , 7 , 8 ]. Indeed, as postulated by the C-value paradox, the complexity of an organism is not related to the amount of DNA, because not all DNA is made up of genes, but it is mostly constituted by intergenic non-coding DNA, and in particular by repetitive DNA [ 9 ].…”