Skip to main content

Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi

Chromosome Research volume 28, pages 139–153 (2020)Cite this article

Abstract

Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach to study the organization and diversification of repetitive elements in some species of these genera. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons, especially Ogre and Chromovirus elements, making up most of genomes, other than P. acutifolius and Vigna species. Satellite DNAs (SatDNAs) were less representative, but highly diverse among species, showing a clear phylogenetic relationship. In situ localization revealed preferential location at pericentromeres and centromeres for both types of sequences, suggesting a heterogeneous composition, especially for centromeres. Few elements showed subterminal accumulation. Copy number variation among chromosomes within and among species was observed for all nine identified SatDNAs. Altogether, our data pointed two main elements (Ty3/Gypsy retrotransponsons and SatDNAs) to the diversification on the repetitive landscape in Phaseoleae, with a typical set of repeats in each species. The high turnover of these sequences, however, did not affect total genome size.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6.

Abbreviations

BAC:

Bacterial artificial chromosome

BLAST:

Basic local alignment search tool

CCD:

Charge-coupled device

CTAB:

Cetrimonium bromide

DAPI:

4',6-diamidino-2-phenylindole

DNA:

Deoxyribonucleic acid

GE:

General Electric

IPTG:

Isopropyl β-D-1-thiogalactopyranoside

LB:

Lysogeny broth

LINE:

Long interspersed nuclear elements

LTR:

Long terminal repeat

NCBI:

National Center for Biotechnology Information

PCR:

Polymerase chain reaction

SSC:

Saline-sodium citrate

TBT:

Trehalose, bovine serum albumin (BSA), and polysorbate-20 (Tween-20)

X-gal:

5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside

References

Download references

Acknowledgments

We thank Embrapa Recursos Genéticos e Biotecnologia (Brasília, Brazil) and the Genebank of the IPK (Gatersleben, Germany) for providing the seeds, and the Platform of Sequencing-LABCEN/CCB at UFPE for the use of its facilities. We are also grateful to the two anonymous reviewers for the critical reading and helpful comments on the manuscript.

Funding

A. Pedrosa-Harand received financial support from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil.

Author information

Affiliations

  1. Integrative Plant Research Laboratory, Department of Botany and Ecology, Federal University of Mato Grosso, Av. Fernando Corrêa da Costa, 2367, Boa Esperança, Cuiabá, MT, 78060900, Brazil

    Tiago Ribeiro

  2. Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Recife, PE, Brazil

    Emanuelle Vasconcelos & Ana Christina Brasileiro-Vidal

  3. Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rêgo, s/n, Cidade Universitária, Recife, PE, 50670420, Brazil

    Karla G. B. dos Santos & Andrea Pedrosa-Harand

  4. Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay

    Magdalena Vaio

Authors
  1. Tiago Ribeiro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emanuelle Vasconcelos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Karla G. B. dos Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Magdalena Vaio
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ana Christina Brasileiro-Vidal
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrea Pedrosa-Harand
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

ACBV, APH, and TR conceived and designed the research. EV, KGBS, MV, and TR conducted the experiments and analyzed the data. TR wrote the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Tiago Ribeiro or Andrea Pedrosa-Harand.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Responsible Editor: Jiming Jiang

Electronic supplementary material

ESM 1

(DOC 1534 kb)

ESM 2

(DOC 29 kb)

ESM 3

(DOC 40 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ribeiro, T., Vasconcelos, E., dos Santos, K.G.B. et al. Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Chromosome Res 28, 139–153 (2020). https://doi.org/10.1007/s10577-019-09618-w

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10577-019-09618-w

Keywords

  • Chromosomal distribution
  • genome composition
  • next-generation sequencing
  • Phaseoleae
  • satellite repeats
  • transposable elements