Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Abstract

BackgroundTransposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes.ResultsPhysical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6.ConclusionOur data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins.

Genomic Organization Under Different Environmental Conditions:Hoplosternum Littoraleas a Model

“…[82][83][84] Association between 18S rDNA and Rex3 are observed in the present study and can be related to dispersion of ribosomal sites, as have previously been observed in other Amazonian fish species. 12,85 Thus, probably 5S rDNA sites were duplicated and dispersed in the genome, since TEs are able to remove and insert themselves at other sites in the genome and are often duplicated during this process. 86 They may generate polymorphisms at their insertion site and exhibit intra-and interspecies copy number variation, or this variability observed in 5S rDNA sites in H. littorale individuals of polluted and unpolluted environments may be related to population differences.…”

“…7,8 Repetitive DNA sequences play key roles in adaptive processes in many organisms because they are less vulnerable to selective pressures compared to single-copy sequences. 4,5,[8][9][10][11][12] Such adaptive processes may be related to genetic variability, which enables a population to adapt to an environment. 13,14 However, the environment has experienced severe damage resulting from anthropic activity, 15 and aquatic biota is constantly exposed to numerous toxic substances released daily into the water.…”

Preferential accumulation of sex and Bs chromosomes in biarmed karyotypes by meiotic drive and rates of chromosomal changes in fishes

“…Although further investigations are needed to clarify the factors involved in the meiotic drive mechanism, repetitive sequences may play a role in this process. Indeed, repetitive DNA sequences have been identified as a promoter of high dynamism in the karyotypes of some groups of Perciformes (Molina 2007, Schneider et al 2013). …”

Chromosome mapping of retrotransposable elementsRex1andRex3inLeporinusSpix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome

“…The retrotransposable elements in the Rex family have been studied widely in some fish groups, including Cichlidae, [9][10][11][12][13][14] Tetraodontidae, [15][16][17] Nototheniidae, Artedidraconidae, Bathydraconidae, Bovichtidae, 18 and Loricariidae. 19 The Rex family elements have a high diversity of chromosome locations in previously studied fish species, and it has been hypothesized that they may have roles in genome differentiation and evolution.…”

“…19 The Rex family elements have a high diversity of chromosome locations in previously studied fish species, and it has been hypothesized that they may have roles in genome differentiation and evolution. [9][10][11][12][13][14][15][16][17]20 However, the characteristics and dynamics of these fish retroelements, which occur mainly in the order Characiformes (a large fish order), still need to be elucidated.…”