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Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA

Planta volume 249, pages 1405–1415 (2019)Cite this article

Abstract

Main conclusion

The most conspicuous difference among chromosomes and genomes in Arachis species, the patterns of heterochromatin, was mainly modeled by differential amplification of different members of one superfamily of satellite DNAs.

Divergence in repetitive DNA is a primary driving force for genome and chromosome evolution. Section Arachis is karyotypically diverse and has six different genomes. Arachis glandulifera (D genome) has the most asymmetric karyotype and the highest reproductive isolation compared to the well-known A and B genome species. These features make A. glandulifera an interesting model species for studying the main repetitive components that accompanied the genome and chromosome diversification in the section. Here, we performed a genome-wide analysis of repetitive sequences in A. glandulifera and investigated the chromosome distribution of the identified satellite DNA sequences (satDNAs). LTR retroelements, mainly the Ty3-gypsy families “Fidel/Feral” and “Pipoka/Pipa”, were the most represented. Comparative analyses with the A and B genomes showed that many of the previously described transposable elements (TEs) were differently represented in the D genome, and that this variation accompanied changes in DNA content. In addition, four major satDNAs were characterized. Agla_CL8sat was the major component of pericentromeric heterochromatin, while Agla_CL39sat, Agla_CL69sat, and Agla_CL122sat were found in heterochromatic and/or euchromatic regions. Even though Agla_CL8sat belong to a different family than that of the major satDNA (ATR-2) found in the heterochromatin of the A, K, and F genomes, both satDNAs are members of the same superfamily. This finding suggests that closely related satDNAs of an ancestral library were differentially amplified leading to the major changes in the heterochromatin patterns that accompanied the karyotype and genome differentiation in Arachis.

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Abbreviations

satDNA:

Satellite DNA

FISH:

Fluorescent in situ hybridization

rDNA:

Ribosomal DNA

LTR:

Long terminal repeat

NGS:

Next-generation sequencing

TEs:

Transposable elements

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Acknowledgements

The authors gratefully acknowledge the financial support from the Agencia Nacional de Promoción Científica y Tecnológica, Argentina (Projects PICT 2007-01875 and PICT 2015-2804); Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina (Project PIP 11220120100192) under the “Exploring the Biological and Genetic Diversity of Arachis Germplasm” program.

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Affiliations

  1. Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina

    Sergio S. Samoluk, Laura M. I. Chalup, Germán Robledo & Guillermo Seijo

  2. Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA

    Carolina Chavarro, David J. Bertioli & Scott A. Jackson

  3. Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina

    Germán Robledo & Guillermo Seijo

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  1. Sergio S. Samoluk
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  2. Laura M. I. Chalup
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  3. Carolina Chavarro
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  4. Germán Robledo
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  7. Guillermo Seijo
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Correspondence to Sergio S. Samoluk.

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Samoluk, S.S., Chalup, L.M.I., Chavarro, C. et al. Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA. Planta 249, 1405–1415 (2019). https://doi.org/10.1007/s00425-019-03096-4

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Keywords

  • Repetitive sequences
  • Chromosome structure
  • Genome evolution
  • Satellite DNA
  • Arachis species