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.
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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
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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.
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A. Pedrosa-Harand received financial support from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil.
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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.
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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
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DOI: https://doi.org/10.1007/s10577-019-09618-w