Phylogenomics of tomato chloroplasts using assembly and alignment-free method

Autores
Amado Cattáneo, Raúl Martín; Diambra, Luis Anibal; Mccarthy, Andrés Norman
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.
Fil: Amado Cattáneo, Raúl Martín. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Diambra, Luis Anibal. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Mccarthy, Andrés Norman. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
Materia
ASSEMBLY AND ALIGNMENT-FREE METHOD
CHLOROPLAST
K-MERS
PHYLOGENOMICS
TOMATO
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/94635
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Phylogenomics of tomato chloroplasts using assembly and alignment-free methodAmado Cattáneo, Raúl MartínDiambra, Luis AnibalMccarthy, Andrés NormanASSEMBLY AND ALIGNMENT-FREE METHODCHLOROPLASTK-MERSPHYLOGENOMICSTOMATOhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.Fil: Amado Cattáneo, Raúl Martín. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Diambra, Luis Anibal. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Mccarthy, Andrés Norman. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaTaylor and Francis Ltd.2018-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/94635Amado Cattáneo, Raúl Martín; Diambra, Luis Anibal; Mccarthy, Andrés Norman; Phylogenomics of tomato chloroplasts using assembly and alignment-free method; Taylor and Francis Ltd.; Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis; 29; 7; 10-2018; 1128-11382470-13942470-1408CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.tandfonline.com/doi/full/10.1080/24701394.2017.1419214info:eu-repo/semantics/altIdentifier/doi/10.1080/24701394.2017.1419214info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-04-15T10:18:04Zoai:ri.conicet.gov.ar:11336/94635instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-04-15 10:18:05.011CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Phylogenomics of tomato chloroplasts using assembly and alignment-free method
title Phylogenomics of tomato chloroplasts using assembly and alignment-free method
spellingShingle Phylogenomics of tomato chloroplasts using assembly and alignment-free method
Amado Cattáneo, Raúl Martín
ASSEMBLY AND ALIGNMENT-FREE METHOD
CHLOROPLAST
K-MERS
PHYLOGENOMICS
TOMATO
title_short Phylogenomics of tomato chloroplasts using assembly and alignment-free method
title_full Phylogenomics of tomato chloroplasts using assembly and alignment-free method
title_fullStr Phylogenomics of tomato chloroplasts using assembly and alignment-free method
title_full_unstemmed Phylogenomics of tomato chloroplasts using assembly and alignment-free method
title_sort Phylogenomics of tomato chloroplasts using assembly and alignment-free method
dc.creator.none.fl_str_mv Amado Cattáneo, Raúl Martín
Diambra, Luis Anibal
Mccarthy, Andrés Norman
author Amado Cattáneo, Raúl Martín
author_facet Amado Cattáneo, Raúl Martín
Diambra, Luis Anibal
Mccarthy, Andrés Norman
author_role author
author2 Diambra, Luis Anibal
Mccarthy, Andrés Norman
author2_role author
author
dc.subject.none.fl_str_mv ASSEMBLY AND ALIGNMENT-FREE METHOD
CHLOROPLAST
K-MERS
PHYLOGENOMICS
TOMATO
topic ASSEMBLY AND ALIGNMENT-FREE METHOD
CHLOROPLAST
K-MERS
PHYLOGENOMICS
TOMATO
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.
Fil: Amado Cattáneo, Raúl Martín. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Diambra, Luis Anibal. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Mccarthy, Andrés Norman. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
description Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.
publishDate 2018
dc.date.none.fl_str_mv 2018-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/94635
Amado Cattáneo, Raúl Martín; Diambra, Luis Anibal; Mccarthy, Andrés Norman; Phylogenomics of tomato chloroplasts using assembly and alignment-free method; Taylor and Francis Ltd.; Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis; 29; 7; 10-2018; 1128-1138
2470-1394
2470-1408
CONICET Digital
CONICET
url http://hdl.handle.net/11336/94635
identifier_str_mv Amado Cattáneo, Raúl Martín; Diambra, Luis Anibal; Mccarthy, Andrés Norman; Phylogenomics of tomato chloroplasts using assembly and alignment-free method; Taylor and Francis Ltd.; Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis; 29; 7; 10-2018; 1128-1138
2470-1394
2470-1408
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.tandfonline.com/doi/full/10.1080/24701394.2017.1419214
info:eu-repo/semantics/altIdentifier/doi/10.1080/24701394.2017.1419214
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Taylor and Francis Ltd.
publisher.none.fl_str_mv Taylor and Francis Ltd.
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1862632249981140992
score 13.203462

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