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Quantitative and qualitative genomic characterization of cultivated Ilex L. species

Published online by Cambridge University Press:  26 June 2014

Alexandra Marina Gottlieb  and
Lidia Poggio
Alexandra Marina Gottlieb*
Affiliation:
Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (UBA-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes y Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, C1428EHACiudad Autónoma de Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Rivadavia 1917, C1033AAJCiudad Autónoma de Buenos Aires, Argentina
Lidia Poggio
Affiliation:
Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (UBA-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes y Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, C1428EHACiudad Autónoma de Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Rivadavia 1917, C1033AAJCiudad Autónoma de Buenos Aires, Argentina
*
*Corresponding author. E-mail: gottlieb@ege.fcen.uba.ar
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Abstract

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

Keywords

flow cytometrygenome filter hybridizationrepresentational difference analysisreverse dot-blot hybridization
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 2 , August 2015 , pp. 142 - 152
Copyright
Copyright © NIAB 2014 

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