Molecular organization of 5S rDNA in sharks of the genusRhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

Abstract

SummaryIn this study, we attempted a molecular characterization of the 5S rDNA in two closely related species of carcharhiniform sharks, Rhizoprionodon lalandii and Rhizoprionodon porosus, as well as a further comparative analysis of available data on lampreys, several fish groups and other vertebrates. Our data show that Rhizoprionodon sharks carry two 5S rDNA classes in their genomes : a short repeat class (termed class I) composed of y185 bp repeats, and a large repeat class (termed class II) arrayed in y465 bp units. These classes were differentiated by several base substitutions in the 5S coding region and by completely distinct non-transcribed spacers (NTS). In class II, both species showed a similar composition for both the gene coding region and the NTS region. In contrast, class I varied extensively both within and between the two shark species. A comparative analysis of 5S rRNA gene sequences of elasmobranchs and other vertebrates showed that class I is closely related to the bony fishes, whereas the class II gene formed a separate cartilaginous clade. The presence of two variant classes of 5S rDNA in sharks likely maintains the tendency for dual ribosomal classes observed in other fish species. The present data regarding the 5S rDNA organization provide insights into the dynamics and evolution of this multigene family in the fish genome, and they may also be useful in clarifying aspects of vertebrate genome evolution.

Molecular organization of the 5S rDNA gene type II in elasmobranchs

“…13,14,60 This suggests a possible influence on the level of transcription. However, despite the presence of a TATA-like box in Rhizoprionodon (with an AATT motif starting at nucleotide -27) 10 and in Rajiformes (as TACA at nucleotide -25), 9 in both Urotrygon species there is not a TATA-like element within the positions ¡30 and ¡20 (5 0 -TGTGAAGAGGC-3') similar to those reported previously in Rhizoprionodon and Rajiformes. This discrepancy in both sequence and location with respect to a TATA-like box among the 3 orders may indicate that these TATA-like boxes are not really essential factors.…”

“…7 These three elements are grouped in the Internal Control Region (ICR) 8 and in elasmobranchs (shark, rays, and skates) have been reported to be respectively at positions 50 -64, 67 -72, and 80 -97 bp of the transcript. 9,10 The transcribed region also contains a termination signal consisting of a poly-T relic, that is still recognized by RNA polymerases III during transcription. Another feature of 5S rDNA is that a TATA box is not strictly required for transcription.…”

“…5,12 In some fish species and in elasmobranchs, 5S rDNA has a TATA-like sequence, suggesting that this sequence influences gene expression. 9,10,13,14,15,16 This TATA-like element in fish has not been experimentally investigated yet. In Xenopus borealis a deletion of 55 nucleotides in the upstream 5 0 end of the 5S rRNA only expressed a part of the gene, showing that this region influences in the transcription process.…”

Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids

“…Unlike the 5S rRNA gene, the NTS is selectively neutral and is characterized by high sequence dynamism, by the presence of insertions/deletions (indels), microsatellites and pseudo-genes (Wasko et al, 2001;Ferreira et al, 2007;Gornung et al, 2007). The occurrence of microsatellites in the NTSs has been reported in several marine organisms (Ota et al, 2003;Alves-Costa et al, 2006), and it seems to be a common feature in the Chondrichthyes group (Rocco et al, 2005;Pasolini et al, 2006;Pinhal et al, 2009). Some authors have suggested that the presence of microsatellite sequences favours the maintenance of tandem arrays of multigene families (Liao and Weiner, 1995;Úbeda-Manzanaro et al, 2010b).…”

“…The microsatellite found in D. labrax and D. punctatus could have this role, and this would explain the low intragenomic variability found. Two variants of 5S rDNA have commonly been found in fishes, characterized by length and sequence differences in the NTS (Martins and Wasko, 2004;Campo et al, 2009;Fujiwara et al, 2009;Pinhal et al, 2009). …”