Skip to main content
SpringerLink
Log in

Isolation and characterization of 5S rDNA sequences in catfishes genome (Heptapteridae and Pseudopimelodidae): perspectives for rDNA studies in fish by C0t method

  • Original Article
  • Published:
Cytotechnology Aims and scope Submit manuscript

Abstract

Sequences of 5S ribosomal RNA (rRNA) are extensively used in fish cytogenomic studies, once they have a flexible organization at the chromosomal level, showing inter- and intra-specific variation in number and position in karyotypes. Sequences from the genome of Imparfinis schubarti (Heptapteridae) were isolated, aiming to understand the organization of 5S rDNA families in the fish genome. The isolation of 5S rDNA from the genome of I. schubarti was carried out by reassociation kinetics (C0t) and PCR amplification. The obtained sequences were cloned for the construction of a micro-library. The obtained clones were sequenced and hybridized in I. schubarti and Microglanis cottoides (Pseudopimelodidae) for chromosome mapping. An analysis of the sequence alignments with other fish groups was accomplished. Both methods were effective when using 5S rDNA for hybridization in I. schubarti genome. However, the C0t method enabled the use of a complete 5S rRNA gene, which was also successful in the hybridization of M. cottoides. Nevertheless, this gene was obtained only partially by PCR. The hybridization results and sequence analyses showed that intact 5S regions are more appropriate for the probe operation, due to conserved structure and motifs. This study contributes to a better understanding of the organization of multigene families in catfish’s genomes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  Google Scholar 

  • Alves-Costa FA, Wasko AP, Oliveira C, Foresti F, Martins C (2006) Genomic organization and evolution of the 5S ribosomal DNA in Tilapiini fishes. Genetica 127:243–252

    Article  CAS  Google Scholar 

  • Ardura A, Pola IG, Linde AR, Garcia-Vazquez E (2010) DNA-based methods for species authentication of Amazonian commercial fish. Food Res Int 43:2295–2302

    Article  CAS  Google Scholar 

  • Barbosa P, Oliveira LA, Pucci MB, Santos MH, Moreira-Filho O, Vicari MR, Nogaroto V, Almeida MC, Artoni RF (2015) Identification and chromosome mapping of repetitive elements in the Astyanax scabripinnis (Teleostei: Characidae) species complex. Genetica 143:55–62

    Article  Google Scholar 

  • Bertollo LAC, Takahashi CS, Moreira-Filho O (1978) Cytotaxonomic considerations on Hopliaslacerdae (Pisces, Erythrinidae). Bras J Genet 1:103–120

    Google Scholar 

  • Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41:226–232

    Article  Google Scholar 

  • Cohen S, Segal D (2009) Extra chromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats. Cytogenet Genome Res 124:327–338

    Article  CAS  Google Scholar 

  • Eickbush TH, Eickbush DG (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477–485

    Article  CAS  Google Scholar 

  • Ferreira IA, Martins C (2008) Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromisniloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes. Micron 39:411–428

    Article  CAS  Google Scholar 

  • Ferreira M, Kavalco KF, Almeida-Toledo LF, Garcia C (2014) Cryptic diversity between two Imparfinis species (Siluriformes, Heptapteridae) by cytogenetic analysis and DNA barcodin. Zebrafish 11:4

    Article  Google Scholar 

  • Garcia CO, Almeida-Toledo LF (2010a) Karyotypic evolution trends in Rhamdiaquelen (Siluriformes, Heptapteridae) with considerations about the origin and differentiation of its supernumerary chromosomes. Genet Mol Res 9:365–384

    Article  CAS  Google Scholar 

  • Garcia CO, Almeida-Toledo LF (2010b) Comparative chromosomal analyses in species of the genus Pimelodella (Siluriformes, Heptapteridae): occurrence of structural and numerical polymorphisms. Caryologia 63:32–40

    Article  Google Scholar 

  • Gouveia JG, Moraes VPO, Sampaio TR, Rosa R, Dias AL (2013) Considerations on karyotype evolution in the genera Imparfinis Eigenmann and Norris 1900 and Pimelodella Eigenmann and Eigenmann 1888 (Siluriformes: Heptapteridae). Rev Fish Biol Fish 23:215–227

    Article  Google Scholar 

  • Gouveia JG, Moraes VPO, Pires LB, Rosa R, Dias AL (2015) Comparative cytogenetics between two species of the family Pseudopimelodidae (Siluriformes): occurrence of natural triploidy and supernumerary chromosomes. Cytotechnology 67:215–522

    Article  Google Scholar 

  • Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:70–74

    Article  Google Scholar 

  • Huang X (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  Google Scholar 

  • Kantek DLZ, Peres WAM, Buckup PA, Moreira-Filho O (2009) Cytogenetics of Imparfinisschubarti (Siluriformes: Heptapteridae) from the Piumhi drainage, a diverted river in Minas Gerais State, Brazil. Zoologia 26:733–738

    Article  Google Scholar 

  • Kapitonov VV, Jurka J (2003) A novel class of SINE elements derived from 5S rDNA. Mol Biol Evol 20:694–702

    Article  CAS  Google Scholar 

  • Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  Google Scholar 

  • Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinform 7:474

    Article  Google Scholar 

  • Long EO, David ID (1980) Repeated genes in eukaryotes. Ann Rev Biochem 49:727–764

    Article  CAS  Google Scholar 

  • Mantovani M, Abel LDS, Moreira-Filho O (2005) Conserved 5S and variable 45S rDNA chromosomal localisation revealed by FISH in Astyanax scabripinnis (Pisces, Characidae). Genetica 123:211–216

    Article  CAS  Google Scholar 

  • Marques MBA, Moreira-Filho O, Garcia C, Margarido VP (2008) Cytogenetic analyses of two endemic fish species from the São Francisco river basin: Conorhynchus conirostris and Lophiosilurus alexandri (Siluriformes). Genet Mol Biol 31:215–221

    Article  Google Scholar 

  • Martinez JF, Lui RL, Blanco DR, Traldi JB, Silva LF, Venere PC, Souza IL, Moreira-Filho O (2011) Comparative cytogenetics of three populations from the Rhamdia quelen species complex (Siluriformes, Heptapteridae) in two Brazilian hydrographic basins. Caryologia 64:121–128

    Article  Google Scholar 

  • Martins C, Galetti PM Jr (1999) Chromosomal localization of 5S rDNA genes in Leporinus fish (Anostomidae, Characiformes). Chromosome Res 7:363–367

    Article  CAS  Google Scholar 

  • Martins C, Galetti PM Jr (2001) Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers. Genome 44:903–910

    Article  CAS  Google Scholar 

  • Martins C, Wasko AP (2004) Organization and evolution of 5S ribosomal DNA in the fish genome. In: Williams CR (ed) Focus on genome research. Nova Science Publishers, pp 335–363

  • Merlo MA, Cross I, Manchado M, Cárdenas S, Rebordinos L (2013) The 5S rDNA high dynamism in Diplodussargus is a transposon-mediatedmechanism. Comparison with other multigene families and Sparidae species. J Mol Evol 76:83–97

    Article  CAS  Google Scholar 

  • Nakajima RT, Cabral-de-Mello DC, Valente GT, Venere PC, Martins C (2012) Evolutionary dynamics of rRNA gene clusters in cichlid fish. BMC Evol Biol 12:198

    Article  CAS  Google Scholar 

  • Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935

    Article  CAS  Google Scholar 

  • Okonechnikov K, Golosova O, Fursov M (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167

    Article  CAS  Google Scholar 

  • Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 83:2934–2938

    Article  CAS  Google Scholar 

  • Raskina O, Belyayev A, Nevo E (2004) Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc Natl Acad Sci USA 101:14818–14823

    Article  CAS  Google Scholar 

  • Rebordinos L, Cross I, Merlo A (2013) High evolutionary dynamism in 5S rDNA of fish: state of the Art. Cytogenet Genome Res 141:103–113

    Article  CAS  Google Scholar 

  • Rodrigues D, Rivera M, Lourenço L (2012) Molecular organization and chromosomal localization of 5S rDNA in Amazonian Engystomops (Anura, Leiuperidae). BMC Genet 13:1–17

    Article  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Sczepanski TS, Vicari MR, Almeida MC, Nogaroto V, Artoni RF (2013) Chromosomal organization of repetitive DNA in Sorubim lima (Teleostei; Pimelodidae). Cytogenet Genome Res 141:309–316

    Article  CAS  Google Scholar 

  • Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform 4:10–14. doi:10.1002/0471250953.bi0410s25

    Google Scholar 

  • Úbeda-Manzanaro M, Merlo MA, Palazón JL, Sarasquete C, Rebordinos L (2010) Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae. Genome 53:723–730

    Article  Google Scholar 

  • Vicari MR, Nogaroto V, Noleto RB, Cestari MM, Cioffi MB, Almeida MC, Moreira-Filho O, Bertollo LAC, Artoni RF (2010) Satellite DNA and chromosomes in Neotropical fishes: methods, applications and perspectives. J Fish Biol 76:1094–1116

    Article  CAS  Google Scholar 

  • Vierna J, Jensen KT, Martinez-Lage A, Gonzalez-Tizon AM (2012) The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae). Heredity 107:127–142

    Article  Google Scholar 

  • Wang Y, Stumph WE (1995) RNA Polymerase II/III transcription specificity determined by TATA box orientation. Proc Natl Acad Sci USA 19:8606–8610

    Article  Google Scholar 

  • Zwick MS, Hanson RE, Islam-Faridi MN, Stelly DM et al (1997) Arapid procedure for the isolation of C0t–1 DNA from plants. Genome 40:138–142

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors are grateful to Dr. André Luis LaforgaVanzela and Dra. Maria Helena Pelegrinelli Fungaro for support to cloning in this study. This research was supported by a grant from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). This search received permission from Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA) to collect fish specimens.

Author information

Authors and Affiliations

  1. Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil

    Juceli Gonzalez Gouveia, Ivan Rodrigo Wolf, Vivian Patrícia Oliveira de Moraes-Manécolo, Vanessa Belline Bardella, Lara Munique Ferracin, Lucia Giuliano-Caetano, Renata da Rosa & Ana Lúcia Dias

Authors
  1. Juceli Gonzalez Gouveia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivan Rodrigo Wolf
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vivian Patrícia Oliveira de Moraes-Manécolo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Vanessa Belline Bardella
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lara Munique Ferracin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lucia Giuliano-Caetano
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Renata da Rosa
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ana Lúcia Dias
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ana Lúcia Dias.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material S1

PCR amplification of 5S rDNA of Imparfinis schubarti genome in 1 % agarose gel (PDF 95 kb)

Supplementary material S2

Results of CENSOR software shows in sequences with incomplete 5S, similar to the SINE3-1 element (PDF 46 kb)

Supplementary material S3

Prediction of the secondary structure of the 5S rRNA obtained by the C0t method. The color scale indicates the likelihood of the pairings (PDF 106 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gouveia, J.G., Wolf, I.R., de Moraes-Manécolo, V.P.O. et al. Isolation and characterization of 5S rDNA sequences in catfishes genome (Heptapteridae and Pseudopimelodidae): perspectives for rDNA studies in fish by C0t method. Cytotechnology 68, 2711–2720 (2016). https://doi.org/10.1007/s10616-016-9996-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10616-016-9996-8

Keywords

Search

Navigation