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Tribe-specific satellite DNA in non-domestic Bovidae

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An Erratum to this article was published on 11 March 2014

Abstract

Satellite sequences present in the centromeric and pericentric regions of chromosomes represent useful source of information. Changes in satellite DNA composition may coincide with the speciation and serve as valuable markers of phylogenetic relationships. Here, we examined satellite DNA clones isolated by laser microdissection of centromeric regions of 38 bovid species and categorized them into three types. Sat I sequences from members of Bovini/Tragelaphini/Boselaphini are similar to the well-documented 1.715 sat I DNA family. Sat I DNA from Caprini/Alcelaphini/Hippotragini/Reduncini/Aepycerotini/Cephalophini/Antilopini/Neotragini/Oreotragini form the second group homologous to the common 1.714 sat I DNA. The analysis of sat II DNAs isolated in our study confirmed conservativeness of these sequences within Bovidae. Newly described centromeric clones from Madoqua kirkii and Strepsiceros strepsiceros were similar in length and repetitive tandem arrangement but showed no similarity to any other satellite DNA in the GenBank database. Phylogenetic analysis of sat I sequences isolated in our study from 38 bovid species enabled the description of relationships at the subfamily and tribal levels. The maximum likelihood and Bayesian inference analyses showed a basal position of sequences from Oreotragini in the subfamily Antilopinae. According to the Bayesian inference analysis based on the indels in a partitioned mixed model, Antilopinae satellite DNA split into two groups with those from Neotragini as a basal tribe, followed by a stepwise, successive branching of Cephalophini, Aepycerotini and Antilopini sequences. In the second group, Reduncini sequences were basal followed by Caprini, Alcelaphini and Hippotragini.

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Abbreviations

BAC:

Bacterial artificial chromosome

BI:

Bayesian inference

BRU-PCR:

Basic repeat unit obtained by PCR

DOP-PCR:

Degenerate oligonucleotide primed polymerase chain reaction

FISH:

Fluorescence in situ hybridization

LINE:

Long interspersed nuclear element

LTR:

Long terminal repeat

MCMC:

Markov chains Monte Carlo

ML:

Maximum likelihood

NCBI:

National Center for Biotechnology Information

NFA:

Numbers of autosomal arms

RFLP:

Restriction fragment length polymorphism

sat:

Satellite

SINE:

Short interspersed nuclear element

SNP:

Single nucleotide polymorphism

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Acknowledgments

We thank Terence J. Robinson and Anne Ropiquet for kindly providing several samples and for useful comments on a draft of the manuscript. This work was supported by the Ministry of Agriculture of the Czech Republic (project MZE 0002716202), the Grant Agency of the Czech Republic (grant P506/10/0421) and by the project “CEITEC—Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) from European Regional Development Funds.

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Authors and Affiliations

  1. Department of Genetics and Reproduction, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic

    Olga Kopecna, Svatava Kubickova, Halina Cernohorska, Katerina Cabelova & Jiri Rubes

  2. Dvur Kralove Zoo, 544 01, Dvur Kralove n. L., Czech Republic

    Jiri Vahala

  3. Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic

    Natalia Martinkova

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  1. Olga Kopecna
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  2. Svatava Kubickova
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  4. Katerina Cabelova
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  7. Jiri Rubes
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Correspondence to Olga Kopecna.

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Responsible editor: Walther Traut

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Kopecna, O., Kubickova, S., Cernohorska, H. et al. Tribe-specific satellite DNA in non-domestic Bovidae. Chromosome Res 22, 277–291 (2014). https://doi.org/10.1007/s10577-014-9401-4

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