Evolutionary dynamics of rRNA gene clusters in cichlid fish

Abstract

BackgroundAmong multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity.ResultsThe present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes.ConclusionsThe organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.

Comparative cytogenetic mapping of rRNA genes among naked catfishes: implications for genomic evolution in the Bagridae family

“…By contrast, 5S rDNA signals were revealed in 2, 3, and 5 pairs of chromosomes in H. nemurus, H. wyckii, and H. filamentus, respectively. Multiple loci of minor ribosomal genes have been found in some fishes (Martins and Galetti, 2001;Hatanaka and Galetti, 2004;Rocco et al, 2005); variation in the number of 5S rDNA loci has also been observed among other species, such as the red wolf fish Erythrinus erythrinus, which has more than 20 sites (Cioffi et al, 2010), the cichlid Astatotilapia latifasciata, which has 15 clusters (Poleto et al, 2010) and the cichlid Laetacara dorsigera, which has 14 sites (Nakajima et al, 2012), In general, 5S rDNA loci can be found in the interstitial regions of fish chromosomes, and their pattern may represent an ancestral condition or even some advantage for the genome organization of these sequences (Martins and Galetti, 2001). H. wyckioides, M. atrifasciatus, and M. multiradiatus appear to maintain the ancestral location of the 5S rDNA loci, while the other genera studied had 5S rDNA loci at the terminal positions of the chromosomes.…”

Interregional cytogenetic comparisons in Halichoeres and Thalassoma wrasses (Labridae) of coastal and insular regions of the southwestern Atlantic

“…In the two Halichoeres species, all the 5S rDNA sites exhibit a syntenic 18S/5S arrangement. Syntenic arrangements of ribosomal genes are a derived condition in Perciformes (Nakajima et al, 2012;Calado et al, 2014;Costa et al, 2016) and Characiformes (Voltolin et al, 2013), and this exclusive feature in both Halichoeres species demonstrates that this organization does not interfere with the gene function. The similarity in the organization of ribosomal genes in the Thalassoma and Halichoeres genera indicates a symplesiomorphic condition in the Julidini species.…”

Microstructural chromosome reorganization in the genus Trichomycterus (Siluriformes: Trichomycteridae)

“…The importance of transposable elements mediating extensive ribosomal DNA multiplications and spreading has been evidenced by several studies (Nakajima et al, 2012;Pansonato-Alves et al, 2013;Symonová et al, 2013). In general, these elements may be allocated within the intergenic spacers of ribosomal families, or even flanking these regions (Nakajima et al, 2012).…”

“…In general, these elements may be allocated within the intergenic spacers of ribosomal families, or even flanking these regions (Nakajima et al, 2012). The considerable variation in chromosomal location of 5S rDNA sites in Trichomycterus suggest that this ribosomal gene may be associated with transposable elements, which might have favored the spreading of these sites in the different species.…”