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Retroelements and DNA Methylation Could Contribute to Diversity of 5S rDNA in Agave L.

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Abstract

Agave L. is a genus of economic importance, and many of the 166 species in the American plant genus Agave L. inhabit high-stress environments, which makes the genus promising for facing global climate change. However, sustainable use of economically important species without interfering with their ecology and evolution requires generating knowledge about the factors responsible for their genetic variation and diversity and, on this basis, their adaptation and speciation. Few genetic studies exploring the evolutionary relationships, speciation processes, genetic variability and diversity within species of Agave are currently available. Analyses of rDNA loci have been performed with the purpose of determining the genetic variability and diversity of the genus Agave, and these loci have been used as genetic markers of ploidy. However, the factors involved in the diversity of 5S rDNA regions in Agave have not yet been studied in depth. Our study explored the possible mechanisms of genetic (retroelements) and epigenetic (DNA methylation) diversity in 5S rDNA regions in Agave. We characterized the 5S rDNA gene tandem in species of the genus with different ploidy numbers and determined the levels of methylation in 13 haplotypes of 5S rDNA and in four non-transcribed spacers (NTS). Our results showed highly dynamic methylation with a high percentage in haplotypes and NTS of 5S rDNA regions in Agave. The characterization of the 5S rDNA tandem array in Agave revealed vestigial remains of the Cassandra terminal-repeat retrotransposon in miniature (TRIM). Our analysis supported previous results suggesting that in species of Agave L., regulation and diversity of 5S rDNA regions are controlled by coordinated genetic and epigenetic events, which will vary according to the species and the level of ploidy. The artificial pressure to which some agave crops are subjected may affect the mechanisms of evolution of gene 5S rDNA.

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Acknowledgements

The authors wish to express their gratitude to M.C. Miriam Monforte González for her contribution and orientation to the sequencing services for clones from the BIBAC genomic library of A. tequilana. Thanks are also given to Dr. Benjamin Abraham Ayil Gutierrez for his contribution in the figures and to M.C. Erika A. De la Cruz-Arguijo for her technical assistance in the sequencing of the clones using the ABI PRISM model 377 sequencer.

Funding

This work was supported by projects 50268 and 180757 of the Center of Scientific Research of Yucatán and the Genomic Biotechnology Center of the National Polytechnic Institute.

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  1. Y. J. Tamayo-Ordóñez and J. A. Narváez-Zapata are co-first authors, these authors contributed equally to this investigation.

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  1. Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico

    Y. J. Tamayo-Ordóñez, M. C. Tamayo-Ordóñez & L. F. Sánchez-Teyer

  2. Instituto Politécnico Nacional (IPN), Centro de Biotecnología Genómica (CBG-IPN), Blvd del Maestro s/n esq., Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa, Tamaulipas, Mexico

    J. A. Narváez-Zapata

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Tamayo-Ordóñez, Y.J., Narváez-Zapata, J.A., Tamayo-Ordóñez, M.C. et al. Retroelements and DNA Methylation Could Contribute to Diversity of 5S rDNA in Agave L.. J Mol Evol 86, 404–423 (2018). https://doi.org/10.1007/s00239-018-9856-6

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