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Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species

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Abstract

Main conclusion

Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids.

The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.

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Abbreviations

DAPI:

4′,6-Diamidino-2-phenylindole

FISH:

Fluorescent in situ hybridization

GISH:

Genome in situ hybridization

LTR:

Long terminal repeat

MYA:

Million years ago

rDNA:

Ribosomal DNA

satDNA:

Satellite DNA

RepeatExplorer2:

RE2

MULEs:

Mutator-like elements

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Acknowledgements

This work was supported by Grants (PICT 2017-3220; PICT 2018-3664) of Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. We thank United States Department of Agriculture (USDA) for providing seeds of some accessions and Center for Applied Genetic Technologies, University of Georgia (Athens, GA, USA), for supporting the genome sequencing.

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Authors and Affiliations

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

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

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

    Magdalena Vaio

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

    Germán Robledo & Guillermo Seijo

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

    David J. Bertioli

Authors
  1. Sergio S. Samoluk
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  2. Magdalena Vaio
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  3. Alejandra M. Ortíz
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  4. Laura M. I. Chalup
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  5. 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., Vaio, M., Ortíz, A.M. et al. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. Planta 256, 50 (2022). https://doi.org/10.1007/s00425-022-03961-9

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