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

ABSTRACT: The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.

SUBMITTER: Castro SI

PROVIDER: S-EPMC4841605 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Castro Sergio I SI Hleap Jose S JS Cárdenas Heiber H Blouin Christian C

RNA biology 20151021 4

The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. ...[more]

PMID: 26488198

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Project description:BackgroundFor anurans, knowledge of 5S rDNA is scarce. For Engystomops species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species Engystomops freibergi and Engystomops petersi, and to extend the knowledge of 5S rDNA organization in anurans, the 5S rDNA sequences of Amazonian Engystomops species were isolated, characterized, and mapped.ResultsTwo types of 5S rDNA, which were readily differentiated by their NTS (non-transcribed spacer) sizes and compositions, were isolated from specimens of E. freibergi from Brazil and E. petersi from two Ecuadorian localities (Puyo and Yasuní). In the E. freibergi karyotypes, the entire type I 5S rDNA repeating unit hybridized to the pericentromeric region of 3p, whereas the entire type II 5S rDNA repeating unit mapped to the distal region of 6q, suggesting a differential localization of these sequences. The type I NTS probe clearly detected the 3p pericentromeric region in the karyotypes of E. freibergi and E. petersi from Puyo and the 5p pericentromeric region in the karyotype of E. petersi from Yasuní, but no distal or interstitial signals were observed. Interestingly, this probe also detected many centromeric regions in the three karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA. The type II NTS probe detected only distal 6q regions in the three karyotypes, corroborating the differential distribution of the two types of 5S rDNA.ConclusionsBecause the 5S rDNA types found in Engystomops are related to those of Physalaemus with respect to their nucleotide sequences and chromosomal locations, their origin likely preceded the evolutionary divergence of these genera. In addition, our data indicated homeology between Chromosome 5 in E. petersi from Yasuní and Chromosomes 3 in E. freibergi and E. petersi from Puyo. In addition, the chromosomal location of the type II 5S rDNA corroborates the hypothesis that the Chromosomes 6 of E. petersi and E. freibergi are homeologous despite the great differences observed between the karyotypes of the Yasuní specimens and the others.

Project description:BackgroundThe multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat.ResultsThree BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors.ConclusionA detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions.

Project description:Yan-Horn Lee, Tsair-Bor Yen, Chiu-Fen Chen, and Mei-Chen Tseng (2018) Thunnus tunas in Scombridae are divided into the temperate subgenus Thunnus (bluefin group) and tropical subgenus Neothunnus (yellowfin group) species based on anatomic traits and distributions. The main purpose of this study was to examine the systematic status of T. obesus based on karyotype, cytochrome (Cyt) b gene, and 5S ribosomal DNA sequences. All T. obesus, T. albacares, T. alalunga, and T. orientalis specimens were caught in southeastern coastal waters off the main island of Taiwan. The karyotypical formula of T. obesus was 2 m + 2 st + 44 t, that of T. albacares was 2 m + 2 sm + 2 st + 42 t, that of T. alalunga was 2 m + 2 sm + 2 st + 42 t, and that of T. orientalis was 2 m + 2 sm + 44 t (m: metacentric; sm: submetacentric; st: subtelocentric; t: telocentric chromosome). According to a molecular genetics analysis for these species using Cyt b gene sequences (1141 bp), interspecific genetic distances ranged from 0.004 (T. orientalis vs. T. alalunga) to 0.038 (T. alalunga vs. T. obesus). The genealogy tree exhibited these 4 species as being categorized into 4 monophyletic groups with high bootstrapping values; T. alalunga and T. orientalis are sister species. This result suggests that the species currently allocated in Thunnus and Neothunnus might need new taxonomic characters to redefine the monophyly of the two subgenera. The sequence lengths of all cloned 5S genes from the 4 species ranged from 327-342 bp. Interspecific genetic distances ranged from 0.016 (T. orientalis vs. T. alalunga) to 0.111 (T. orientalis vs. T. albacares). The phylogenetic tree based on 5S rDNA shows T. obesus divided into 2 groups: one similar to T. albacares and the other close to T. orientalis. These results imply that Thunnus tunas have a common synapomorphic character with Scombridae fish (2n = 48) and high numbers of telocentric chromosomes (42-44). Thunnus orientalis and T. alalunga are sister based on molecular data. Thunnus obesus may have been derived from a more-complicated speciation processes.

Dataset Information

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

Publications

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

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