Intraindividual and Interspecies Variation in the 5S rDNA of Coregonid Fish

Abstract

This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate DNA sequence for comparisons of closely related taxa.

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

“…However, NTS II also separated R. lalandii from R. porosus in phylogenetic trees, due to five consistent base substitutions, showing that the NTS II can be useful for phylogenetic inference in shark species. This result is in agreement with those obtained for the neotropical characiform Leporinus (Ferreira et al, 2006) and Brycon (Wasko et al, 2001), in which the NTS effectively separated closely related species, but it contrasts with the results obtained by Pasolini et al (2006) for the equivalent NTS II existing in rays, as well as those by Robles et al (2005) for sturgeons and by Sajdak et al (1998) for Coregonus. In view of these contradictory results, NTS sequences must be used with caution in evolutionary surveys.…”

“…In this context, it has been recently demonstrated that the presence of conserved elements located within this NTS also plays an important role in the regulation of the 5S gene expression in mammals (Nederby-Nielsen et al, 1993;Hallenberg & Frederiksen, 2001). In fishes, a conserved TATA-like sequence has been observed upstream of the 5S gene in several teleosts, including Salmo salar (Penda´s et al, 1994), Carassius auratus (Murakami & Fugitani, 1998), Coregonus (Sajdak et al, 1998), Gasterosteus aculeatus (Rocco et al, 1999), Acheilognathus tabira and Cyprinus carpio (Inafuku et al, 2000), O. niloticus (Martins et al, 2000), Brycon (Wasko et al, 2001) and Leporinus , suggesting a possible influence on the transcription level of this gene. In elasmobranchs, such sequences were also detected in Rajidae (Pasolini et al, 2006), but no data regarding sharks have been reported previously.…”

Localization and Characterization of the 5S rDNA Bearing Chromosome in Two Steindachneridion Species by Means of Different Cytogenetic Techniques

“…Moreover, the NOR and 5S rDNA sites may assume a syntenical organization in the same chromosome, e.g., in Salmo salar, Oncorhynchus mykiss and Parodon tortuosus (Pendás et al 1994, Vicente et al 2001, or can be detected more frequently in different chromosomes (Martinez et al 1996, Sadjak et al 1998.…”

Discrimination of Shark species by simple PCR of 5S rDNA repeats

“…Moreover, the distinct genome organization patterns of the 5S rDNA tandem repeats have been also useful as genetic markers not only in evolutionary studies but also in practical approaches for the discrimination of fish species (Pendas et al, 1995;Sajdak et al, 1998;Céspedes et al, 1999;Asensio et al, 2001), even for species of the same genus (Perez and Garcia-Vázquez, 2004;Aranishi, 2005). Nonetheless, there are no data about the usefulness of the 5S rDNA as genetic marker in the elasmobranch fish group.…”

“…This is probably due to major differences in the sharks' NTS organization, since the coding region was found to be conserved in other cartilaginous fishes (Pasolini et al, 2006). Nucleotide sequence analyses based on the NTS have shown that the great variability found in this region can be due to insertions/deletions, minirepeats, and pseudogenes (Nelson and Honda, 1985;Leah et al, 1990;Sajdak et al, 1998).…”