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Comparative Characterization of Ribosomal DNA Regions in Different Agave Accessions with Economical Importance

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Abstract

Two ribosomal DNA regions (5S and 18S) were characterized in three economically important species of Agave Linnaeus, 1753 namely Agave tequilana Weber, 1902; Agave angustifolia Haworth, 1915; and Agave fourcroydes Lemaire, 1864 which are used to produce several products such as tequila, mezcal, and hard fibers. Characterization included Agave L. accessions with different ploidy levels (2n = 2x = 60 to 2n = 6 × = 180) in order to relate this factor with copy number, haplotype number, expression profile, and predictable functionality of ribosomal DNA (rDNA) sequences. Only total rDNA copy number (5S and 18S) was related with ploidy level. Main differences were found in the 5S rDNA gene since it exhibited different genetic traits of Agave L. accession. In this gene, four different allelic groups (I, 105; II, 107; III, 110; and IV, 111 bp) were detected, which have probably evolved separately, thus exhibiting different expression profiles and different haplotype occurrence. Allelic groups III and IV exhibit the highest number of total and expressed copies in all Agave L. accessions. Non-redundant haplotypes were probably more functional in these allelic groups. Differences between the Agave L. accessions were more clearly observed in the most cultivated accession, A. tequilana (2n = 2 × = 60), where the allelic group III shows non-redundant haplotypes and is transcriptionally upregulated suggesting a different evolutionary pressure on this Agave L. accession.

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Acknowledgments

The authors express their gratitude to María Concepción Tamayo Ordóñez, PhD, for her critical revision of the MS and Adriana Quiroz Moreno MC for her technical assistance. This project was supported by the National Council of Science and Technology of Mexico by the projects 50268 and 180757 and the fellow (240190) for the first author.

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Authors and Affiliations

  1. Centro de Investigación Científica de Yucatán A.C., Unidad de Biotecnología, Yucatán, Mexico

    Y. J. Tamayo-Ordóñez & L. F. Sánchez-Teyer

  2. Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Mexico, Mexico

    J. A. Narváez-Zapata

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  1. Y. J. Tamayo-Ordóñez
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  2. J. A. Narváez-Zapata
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  3. L. F. Sánchez-Teyer
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Correspondence to L. F. Sánchez-Teyer.

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Supplementary Figure A

(1) 5S rDNA primer localization for different sequences obtained from Genbank. Accession numbers are JN051136, JX975658, AY544252, HQ270935, U02637, EF071653, EU093377, EU925062, FJ882491, AJ390208, DQ351339 and EF071691 for Elymus sibiricus L., Lycoris radiate L’Hér., Hordeum chilense Roem. et Schultz, Aegilops ventricosa Tausch, Eleusine coracana Gaertner, Avena occidentalis L., Pseudoroegneria spicata Pursh, Aegilop scomosa L., Triticum turgidum L., Helictotrichon versicolor Schult. & Schult. f., Zea mays L. and Avena sativa L., respectively. (2) 18S rDNA primer localization concerning to different sequences obtained from Genbank. Accession numbers are HM640709, JQ283933, JQ283917, JQ283914, AF206841, JQ283900 and GU980213 for Agave ghiesbreghtii Lem., Echeandia sp., Sansevieria trifasciata Prain, Liriope spicata, Agave ghiesbreghtii Lem., Asparagus officinalis and Agave tequilana cultivar Azul, respectively. (3) Actin gene primer localization for different sequences obtained from Genbank. Accession numbers are AY550991, JX826390, HQ148720, NM001153459, HQ395760, AF237626, AK101613, AY014278, JX310699, AK365182, FP099325 and GQ983555 for Elaeis guineensis Jacq, Lilium regale L., Ananas comosus L., Zea mays L., Echinochloa crus-galli L., Vallisneria natans L., Oryza sativa L., Lolium perenne L., Narcissus tazetta L., Hordeum vulgare L, Phyllostachys edulis and Agave tequilana Weber cultivar Azul, respectively. (GIF 468 kb)

High Resolution Image (TIFF 21705 kb)

Supplementary Figure B

Polymorphisms in (1) 5S and 18S (2) rDNA haplotypes. Polymorphism positions are showed according to closest genetic related sequences retrieved from Genbank for 5S (Triticum turgidum; FJ882491) and 18S (Agave tequilana; GU980213) rDNA genes, respectively (GIF 120 kb)

High Resolution Image (TIFF 156 kb)

Supplementary Figure C

Examples of electropherograms obtained from different Agave accessions using 18S rDNA PCR products. (1) A. tequilana Weber (2n=2x=60), (2) A. angustifolia Ham. (2n=2x=60), (3) A. angustifolia Ham. (2n=6x=180), (4) A. fourcroydes Lem. (2n=3x=90) and (5) A. fourcroydes Lem. (2n=5x=150). Allelic peak numbered as 1 was about 187 bp. (GIF 62 kb)

High Resolution Image (TIFF 152 kb)

Supplementary Figure D

5S rDNA copies analysis. Specific 5S rDNA copies per genome for each detected peak in capillary analysis. Error bars represent the standard error (n = 3). Different letters in the bars represent the statistical significance of mean differences between each allelic group in the accessions of Agave L. determination according to the Tukey test (P ≤ 0.05). (GIF 57 kb)

High Resolution Image (TIFF 157 kb)

Supplementary Table A

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Supplementary Table B

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Tamayo-Ordóñez, Y.J., Narváez-Zapata, J.A. & Sánchez-Teyer, L.F. Comparative Characterization of Ribosomal DNA Regions in Different Agave Accessions with Economical Importance. Plant Mol Biol Rep 33, 2014–2029 (2015). https://doi.org/10.1007/s11105-015-0895-5

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