Quantitative and qualitative genomic characterization of cultivated Ilex L. species

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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 methodolo...

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Autores principales: Gottlieb, A.M., Poggio, L.
Formato: JOUR
Materias:
flow cytometry
genome filter hybridization
representational difference analysis
reverse dot-blot hybridization
Ilex
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_14792621_v13_n3_p_Gottlieb
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
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spelling todo:paper_14792621_v13_n3_p_Gottlieb2023-10-03T16:19:30Z Quantitative and qualitative genomic characterization of cultivated Ilex L. species Gottlieb, A.M. Poggio, L. flow cytometry genome filter hybridization representational difference analysis reverse dot-blot hybridization Ilex 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. © 2014 NIAB. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14792621_v13_n3_p_Gottlieb
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic flow cytometry
genome filter hybridization
representational difference analysis
reverse dot-blot hybridization
Ilex
spellingShingle flow cytometry
genome filter hybridization
representational difference analysis
reverse dot-blot hybridization
Ilex
Gottlieb, A.M.
Poggio, L.
Quantitative and qualitative genomic characterization of cultivated Ilex L. species
topic_facet flow cytometry
genome filter hybridization
representational difference analysis
reverse dot-blot hybridization
Ilex
description 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. © 2014 NIAB.
format JOUR
author Gottlieb, A.M.
Poggio, L.
author_facet Gottlieb, A.M.
Poggio, L.
author_sort Gottlieb, A.M.
title Quantitative and qualitative genomic characterization of cultivated Ilex L. species
title_short Quantitative and qualitative genomic characterization of cultivated Ilex L. species
title_full Quantitative and qualitative genomic characterization of cultivated Ilex L. species
title_fullStr Quantitative and qualitative genomic characterization of cultivated Ilex L. species
title_full_unstemmed Quantitative and qualitative genomic characterization of cultivated Ilex L. species
title_sort quantitative and qualitative genomic characterization of cultivated ilex l. species
url http://hdl.handle.net/20.500.12110/paper_14792621_v13_n3_p_Gottlieb
work_keys_str_mv AT gottliebam quantitativeandqualitativegenomiccharacterizationofcultivatedilexlspecies
AT poggiol quantitativeandqualitativegenomiccharacterizationofcultivatedilexlspecies
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