Transposable Elements in Fish Chromosomes: A Study in the Marine Cobia Species

Abstract

Rachycentron canadum, a unique representative of the Rachycentridae family, has been the subject of considerable biotechnological interest due to its potential use in marine fish farming. This species has undergone extensive research concerning the location of genes and multigene families on its chromosomes. Although most of the genome of some organisms is composed of repeated DNA sequences, aspects of the origin and dispersion of these elements are still largely unknown. The physical mapping of repetitive sequences on the chromosomes of R. canadum proved to be relevant for evolutionary and applied purposes. Therefore, here, we present the mapping by fluorescence in situ hybridization of the transposable element (TE) Tol2, the non-LTR retrotransposons Rex1 and Rex3, together with the 18S and 5S rRNA genes in the chromosome of this species. The Tol2 TE, belonging to the family of hAT transposons, is homogeneously distributed in the euchromatic regions of the chromosomes but with huge colocalization with the 18S rDNA sites. The hybridization signals for Rex1 and Rex3 revealed a semi-arbitrary distribution pattern, presenting differentiated dispersion in euchromatic and heterochromatic regions. Rex1 elements are associated preferentially in heterochromatic regions, while Rex3 shows a scarce distribution in the euchromatic regions of the chromosomes. The colocalization of TEs with 18S and 5S rDNA revealed complex chromosomal regions of repetitive sequences. In addition, the nonpreferential distribution of Rex1 and Rex3 in all heterochromatic regions, as well as the preferential distribution of the Tol2 transposon associated with 18S rDNA sequences, reveals a distinct pattern of organization of TEs in the genome of this species. A heterogeneous chromosomal colonization of TEs may confer different evolutionary rates to the heterochromatic regions of this species.

Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum)

“…In Astyanax janeiroensis, the colocalization of 18S rDNA sites with As51 satellite DNA was seen to promote the silencing of ribosomal sites. 45 Similarly, an extensive dispersion of hisDNA H3 and hisDNA H2B-H2A sites was detected on the chromosomes of R. canadum 22 colocalized with some TE, such as Rex1 and Rex3, 20 and with the microsatellite (GA) 15 (present study). This distribution pattern also suggests that not all H3 (48 in total) and H2B-H2A sites (24 in total) could be genetically active, in spite of their generally conserved condition.…”

“…44 Similarly, in R. canadum, the distribution of some microsatellites is also coincident with the Tol2 transposon and Rex1 e Rex3 elements. 20 Thus, the colocalization of microsatellites and TE over extensive areas of the genome also suggests the coevolutionary process of these sequences in this species. In Astyanax janeiroensis, the colocalization of 18S rDNA sites with As51 satellite DNA was seen to promote the silencing of ribosomal sites.…”

“…This distribution pattern also suggests that not all H3 (48 in total) and H2B-H2A sites (24 in total) could be genetically active, in spite of their generally conserved condition. [46][47][48] On the other hand, extensive chromosome mapping of different repetitive sequences in the chromosomes of this species [20][21][22] has shown the functional coexistence between active genetic regions and different repetitive DNA classes.…”

“…18,19 Increasing amounts of cytogenetic data have provided information on its karyotype structure, replication band patterns, and chromosome mapping of telomeric, transposable, and retrotransposable elements, in addition to ribosomal and histone genes. 20,21 The uncommon expansion of a number of repetitive sequences in R. canadum chromosomes 22 suggests a special attention to be given to the composition of heterochromatin and distribution of the microsatellite sequences.…”

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet<b> </b>(<b><i>Acipenser ruthenus</i></b>)

“…Sometimes, large amounts of the repetitive DNAs might promote rDNA silencing [Vicari et al, 2008], although this is not shown in all cases [Costa et al, 2013]. In our case, the enrichment of 2 out of 3 ribosomal gene clusters with repetitive DNAs probably did not affect their activity, as there are 2 active NOR sites in sterlet according to silver staining data.…”