Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools
Background and Aims: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. Methods: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. Key Results: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. Conclusions: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.
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Oxford University Press
2021-06-15T20:02:55Z
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Subjects: | Maíz, Zea mays, Genética, Variación Genética, Fitogenética, Genómica, Maize, Genetics, Genetic Variation, Plant Genetics, Genomics, Whole Plastome Sequencing, Maize Landraces, Intraspecific Variation, Maize Dispersal, |
Online Access: | http://hdl.handle.net/20.500.12123/9592 https://academic.oup.com/aob/advance-article-abstract/doi/10.1093/aob/mcab038/6161338 https://doi.org/10.1093/aob/mcab038 |
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Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal |
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Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal Lopez, Mariana Gabriela Fass, Monica Irina Rivas, Juan Gabriel Carbonell-Caballero, José Vera, Pablo Alfredo Puebla, Andrea Fabiana Defacio, Raquel Alicia Dopazo, Joaquín Paniego, Norma Beatriz Hopp, Horacio Esteban Lia, Verónica Viviana Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
description |
Background and Aims: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers.
Methods: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes.
Key Results: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions.
Conclusions: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers. |
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info:ar-repo/semantics/artículo |
topic_facet |
Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal |
author |
Lopez, Mariana Gabriela Fass, Monica Irina Rivas, Juan Gabriel Carbonell-Caballero, José Vera, Pablo Alfredo Puebla, Andrea Fabiana Defacio, Raquel Alicia Dopazo, Joaquín Paniego, Norma Beatriz Hopp, Horacio Esteban Lia, Verónica Viviana |
author_facet |
Lopez, Mariana Gabriela Fass, Monica Irina Rivas, Juan Gabriel Carbonell-Caballero, José Vera, Pablo Alfredo Puebla, Andrea Fabiana Defacio, Raquel Alicia Dopazo, Joaquín Paniego, Norma Beatriz Hopp, Horacio Esteban Lia, Verónica Viviana |
author_sort |
Lopez, Mariana Gabriela |
title |
Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
title_short |
Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
title_full |
Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
title_fullStr |
Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
title_full_unstemmed |
Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
title_sort |
plastome genomics in south american maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools |
publisher |
Oxford University Press |
publishDate |
2021-06-15T20:02:55Z |
url |
http://hdl.handle.net/20.500.12123/9592 https://academic.oup.com/aob/advance-article-abstract/doi/10.1093/aob/mcab038/6161338 https://doi.org/10.1093/aob/mcab038 |
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oai:localhost:20.500.12123-95922021-06-15T20:35:45Z Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools Lopez, Mariana Gabriela Fass, Monica Irina Rivas, Juan Gabriel Carbonell-Caballero, José Vera, Pablo Alfredo Puebla, Andrea Fabiana Defacio, Raquel Alicia Dopazo, Joaquín Paniego, Norma Beatriz Hopp, Horacio Esteban Lia, Verónica Viviana Maíz Zea mays Genética Variación Genética Fitogenética Genómica Maize Genetics Genetic Variation Plant Genetics Genomics Whole Plastome Sequencing Maize Landraces Intraspecific Variation Maize Dispersal Background and Aims: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. Methods: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. Key Results: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. Conclusions: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers. EEA Pergamino Fil: López, Mariana Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: López, Mariana Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: López, Mariana Gabriela. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Fass, Mónica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fass, Mónica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Fass, Mónica. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Rivas, Juan Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Rivas, Juan Gabriel. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Carbonell-Caballero, José. Centre for Genomic Regulation. Stem Cells and Cancer Program. Gene Regulation; España Fil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Puebla, Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Puebla, Andrea. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Defacio, Raquel Alicia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Banco de Germoplasma; Argentina Fil: Dopazo, Joaquín. Hospital Virgen del Rocío. Centro de Documentación Clínica Avanzada. Fundación Progreso y Salud. Clinical Bioinformatics Area ; España Fil: Paniego, Norma. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paniego, Norma. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Paniego, Norma. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Hopp, Horacio Esteba. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Lia, Verónica Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Lia, Verónica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Lia, Verónica Viviana. Instituto Nacional de Tecnología Agropecuaria-Consejo Nacional de Investigaciones Científicas y Técnicas (INTA-CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Lia, Verónica Viviana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina info:eu-repo/date/embargoEnd/2022-06-15 2021-06-15T20:02:55Z 2021-06-15T20:02:55Z 2021-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion http://hdl.handle.net/20.500.12123/9592 https://academic.oup.com/aob/advance-article-abstract/doi/10.1093/aob/mcab038/6161338 0305-7364 1095-8290 (online) https://doi.org/10.1093/aob/mcab038 eng info:eu-repo/semantics/embargoedAccess application/pdf Oxford University Press Annals of Botany 127 : 1-34. (May 2021) |