Organization of Repeated DNA Elements in the Genome of the Cichlid Fish <i>Cichla kelberi</i> and Its Contributions to the Knowledge of Fish Genomes

Abstract

Repeated DNA elements have been extensively applied as physical chromosome markers in comparative studies for the identification of chromosomal rearrangements, the identification of sex chromosomes, chromosome evolution analysis and applied genetics. Here, we report the characterization of the transposable elements (TE) Tc1, Rex1, Rex3 and Rex6 and a new element called RCk in the genome of the South American cichlid fish Cichla kelberi using nucleotide sequence analysis and hybridization to metaphase chromosomes. The analysis of the repeated elements demonstrated that they are, in most cases, compartmentalized in heterochromatic regions, as has been observed in several other vertebrates. On the other hand, the elements Rex1 and Rex3 were also observed spanning extensive euchromatic regions on 2 chromosome pairs. The RCk element exhibits a wide distribution among fishes and also in amphibians, and it was spread throughout the chromosomes of C. kelberi. Our results have demonstrated that the compartmentalization of repeated elements is not restricted to heterochromatic segments, which has provided new concepts with regard to the genomic organization of transposons.

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

“…10 This was confirmed by the BLASTn analysis where the Rex1 and Rex3 sequences shared high similarity with those of other fish groups, which demonstrates that these elements are fairly well conserved in different families. Previous researchers have suggested that the Rex6 element may have been lost or diverged greatly, depending on the rate of host evolution.…”

“…17 Species in the family Cichlidae are exceptional because the Rex elements are frequently distributed in the pericentromeric regions. [9][10][11][12][13][14] In particular, Rex1 had different chromosome locations in Leporinus species. Leporinus elongatus, L. macrocephalus, and L. obtusidens had isolated signals in terminal positions in all chromosomes.…”

“…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.…”

The role of chromosomal fusion in the karyotypic evolution of the genus Ageneiosus (Siluriformes: Auchenipteridae)

“…The hybridization with the [GATA] n sequence showed correspondence with the heterochromatin in the terminal region of almost all chromosomes, also being present in lower amount in interstitial regions, and coincident with the unique C-band in the pericentromeric region (pair 1). This situation in which repetitive elements have been found widely dispersed in the genomes is relatively common and has been observed in other fish species recently (e.g., Teixeira et al, 2009;Ferreira et al, 2011).…”