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Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A–B genome divergence

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Abstract

Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita. Fluorescent in situ hybridization (FISH) experiments showed that Matita is mainly located on the distal regions of chromosome arms and is of approximately equal frequency on both A- and B-chromosomes. Its chromosome-specific hybridization pattern facilitates the identification of individual chromosomes, a useful cytogenetic tool considering that chromosomes in peanut are mostly metacentric and of similar size. Phylogenetic analysis of Matita elements, molecular dating of transposition events, and an estimation of the evolutionary divergence of the most probable A- and B-donor species suggest that Matita underwent its last major burst of transposition activity at around the same time of the A- and B-genome divergence about 3.5 million years ago. By probing BAC libraries with overgos probes for Matita, resistance gene analogues, and single- or low-copy genes, it was demonstrated that Matita is not randomly distributed in the genome but exhibits a significant tendency of being more abundant near resistance gene homologues than near single-copy genes. The described work is a further step towards broadening the knowledge on genomic and chromosomal structure of peanut and on its evolution.

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Abbreviations

BAC:

Bacterial artificial chromosome

BES:

BAC end-sequences

DAPI:

4′,6-Diamidino-2-phenylindole

EDTA:

Ethylenediaminetetraacetic acid

FISH:

Fluorescent in situ hybridization

FITC:

Fluorescein isothiocyanate

GISH:

Genomic in situ hybridization

LTR:

Long terminal repeat

Mya:

Million years ago

NBS:

Nucleotide-binding site

NOR:

Nucleolar organizer region

ORF:

Open reading frame

PBS:

Primer binding site

PPT:

Poly purine tract

RGA:

Resistance gene analogue

RT:

Reverse transcriptase

SDS:

Sodium dodecyl sulphate

SSC:

Standard saline citrate (1×SSC = 0.15 M NaCl; 0.015 M Na3-citrate)

UTR:

Untranslated region

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Acknowledgments

Stephan Nielen would like to thank the National Council for Scientific and Technological Development of Brazil (CNPq) for a post-doctoral fellowship. Bruna Vidigal is grateful for post-graduate grants from the Brazilian Ministry of Education (CAPES—Coordenação de Aperfeiçoamento de Pessoal de Nível Superior). David Bertioli would also like to thank CNPq for a productivity fellowship. We also thank the Generation Challenge Program (TLI) for supporting this work. We thank José Valls for providing Arachis germplasm.

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Author notes

  1. Stephan Nielen

    Present address: Plant Breeding and Genetics Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria

Authors and Affiliations

  1. Embrapa Recursos Genéticos e Biotecnologia, 70770-917, Brasília, DF, Brazil

    Stephan Nielen, Soraya C. M. Leal-Bertioli & Patricia M. Guimarães

  2. Universidade de Brasília, Campus Universitário, 70910-900, Brasília, DF, Brazil

    Bruna S. Vidigal & David J. Bertioli

  3. Universidade Católica de Brasília, Campus II, SGAN 916, 70790-160, Brasília, DF, Brazil

    Bruna S. Vidigal & David J. Bertioli

  4. Plant Genome Mapping Laboratory, The University of Georgia, Athens, 30605, USA

    Milind Ratnaparkhe & Andrew H. Paterson

  5. Centre de Coopération International en Recherche Agronomique pour le Developpement (CIRAD), Montpellier, France

    Olivier Garsmeur & Angélique D’Hont

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  7. Angélique D’Hont
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Correspondence to Stephan Nielen.

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Communicated by M.-A. Grandbastien.

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Nielen, S., Vidigal, B.S., Leal-Bertioli, S.C.M. et al. Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A–B genome divergence. Mol Genet Genomics 287, 21–38 (2012). https://doi.org/10.1007/s00438-011-0656-6

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  • DOI: https://doi.org/10.1007/s00438-011-0656-6

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