Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa

Autores
Calderón, Franco; Gilslak, Jazmín; Gutierrez, Ángela Verónica; Fortunato, Renee Hersilia; Lia, Veronica Viviana; Morales, Matias
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Mimosa L. is a megadiverse genus where lower rank classification is challenging due to widespread morphological similarities. M. subser. Obstrigosae includes 12 species with different ploidy levels. Morphological boundaries between them are defined by a few traits influenced by the environment. The extreme case is displayed by M. tandilensis and M. ramulosa which are solely defined by differences in plant habit, a trait poorly documented in herbaria. To aid species delimitation and taxonomic resolution in M. subser. Obstrigosae, we intended to develop new microsatellite markers. A ddRAD library was constructed from one individual of each M. tandilensis and M. ramulosa species. NGS derived reads were bioinformatically analysed for SSR mining. In order to avoid other sources of variation rather than the intended allelic variants, manual curation was performed. The applied selection criteria retained 72 loci from 495 candidates. Over 22 primer pairs tested, 15 polymorphic SSR were successfully amplified in a 22 individual panel test. Transferability to other species with varying phylogenetic relatedness was successful. A total of 239 variable characters (alleles), scored as presence-absence matrix, allowed to recognize species membership among 30 individuals belonging to four species of M. subser. Obstrigosae; M. adpressa and M. obstrigosa constitute two clear groups, contrarily to M. tandilensis and M. ramulosa that grouped together in several clusters. This pattern supports the hypothesis that the two latter perform a taxonomic complex, coinciding with conflicts to distinguish them by means of morphology. These results suggest that the 15 loci selected are suitable for clarifying species delimitation within M. subser. Obstrigosae. In sum, SSR development based on NGS sequencing and the selection criteria contributed herein provide a valuable tool for the molecular characterization of Mimosa beyond subseries Obstrigosae and may aid SSR development in other polyploid species.
Instituto de Recursos Biológicos
Fil: Calderón, Franco. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gilszlak, Jazmín. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; Argentina
Fil: Gutiérrez, Angela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; Argentina
Fil: Fortunato, Reneé H. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Academia Nacional de Ciencias Exactas, Físicas y Naturales (IBODA-ANCEFN/CONICET). Instituto de Botánica Darwinion; Argentina
Fil: Lía, Verónica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina
Fil: Morales, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina
Fuente
Systematics and Biodiversity 22 (1) : Article: 2383213. (2024)
Materia
Polyploidy
Genetic Markers
Microsatellites
Poliploidia
Marcadores Genéticos
Mimosa
Microsatélites
High Throughput Sequencing
SSR Development
SSR Transferability
Secuenciación de Alto Rendimiento
Desarrollo SSR
Transferibilidad de la SSR
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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spelling Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus MimosaCalderón, FrancoGilslak, JazmínGutierrez, Ángela VerónicaFortunato, Renee HersiliaLia, Veronica VivianaMorales, MatiasPolyploidyGenetic MarkersMicrosatellitesPoliploidiaMarcadores GenéticosMimosaMicrosatélitesHigh Throughput SequencingSSR DevelopmentSSR TransferabilitySecuenciación de Alto RendimientoDesarrollo SSRTransferibilidad de la SSRMimosa L. is a megadiverse genus where lower rank classification is challenging due to widespread morphological similarities. M. subser. Obstrigosae includes 12 species with different ploidy levels. Morphological boundaries between them are defined by a few traits influenced by the environment. The extreme case is displayed by M. tandilensis and M. ramulosa which are solely defined by differences in plant habit, a trait poorly documented in herbaria. To aid species delimitation and taxonomic resolution in M. subser. Obstrigosae, we intended to develop new microsatellite markers. A ddRAD library was constructed from one individual of each M. tandilensis and M. ramulosa species. NGS derived reads were bioinformatically analysed for SSR mining. In order to avoid other sources of variation rather than the intended allelic variants, manual curation was performed. The applied selection criteria retained 72 loci from 495 candidates. Over 22 primer pairs tested, 15 polymorphic SSR were successfully amplified in a 22 individual panel test. Transferability to other species with varying phylogenetic relatedness was successful. A total of 239 variable characters (alleles), scored as presence-absence matrix, allowed to recognize species membership among 30 individuals belonging to four species of M. subser. Obstrigosae; M. adpressa and M. obstrigosa constitute two clear groups, contrarily to M. tandilensis and M. ramulosa that grouped together in several clusters. This pattern supports the hypothesis that the two latter perform a taxonomic complex, coinciding with conflicts to distinguish them by means of morphology. These results suggest that the 15 loci selected are suitable for clarifying species delimitation within M. subser. Obstrigosae. In sum, SSR development based on NGS sequencing and the selection criteria contributed herein provide a valuable tool for the molecular characterization of Mimosa beyond subseries Obstrigosae and may aid SSR development in other polyploid species.Instituto de Recursos BiológicosFil: Calderón, Franco. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gilszlak, Jazmín. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; ArgentinaFil: Gutiérrez, Angela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; ArgentinaFil: Fortunato, Reneé H. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Academia Nacional de Ciencias Exactas, Físicas y Naturales (IBODA-ANCEFN/CONICET). Instituto de Botánica Darwinion; ArgentinaFil: Lía, Verónica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; ArgentinaFil: Morales, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; ArgentinaTaylor and Francis2024-12-26T11:37:46Z2024-12-26T11:37:46Z2024-09-23info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/20750https://www.tandfonline.com/doi/full/10.1080/14772000.2024.23832131477-20001478-0933https://doi.org/10.1080/14772000.2024.2383213Systematics and Biodiversity 22 (1) : Article: 2383213. (2024)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PD-E2-I038-002, Evaluación, monitoreo y manejo de la biodiversidad en sistemas agropecuarios y forestalesinfo:eu-repograntAgreement/INTA/2023-PD-L01-I087, Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.info:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:50:50Zoai:localhost:20.500.12123/20750instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:50:51.053INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
title Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
spellingShingle Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
Calderón, Franco
Polyploidy
Genetic Markers
Microsatellites
Poliploidia
Marcadores Genéticos
Mimosa
Microsatélites
High Throughput Sequencing
SSR Development
SSR Transferability
Secuenciación de Alto Rendimiento
Desarrollo SSR
Transferibilidad de la SSR
title_short Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
title_full Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
title_fullStr Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
title_full_unstemmed Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
title_sort Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
dc.creator.none.fl_str_mv Calderón, Franco
Gilslak, Jazmín
Gutierrez, Ángela Verónica
Fortunato, Renee Hersilia
Lia, Veronica Viviana
Morales, Matias
author Calderón, Franco
author_facet Calderón, Franco
Gilslak, Jazmín
Gutierrez, Ángela Verónica
Fortunato, Renee Hersilia
Lia, Veronica Viviana
Morales, Matias
author_role author
author2 Gilslak, Jazmín
Gutierrez, Ángela Verónica
Fortunato, Renee Hersilia
Lia, Veronica Viviana
Morales, Matias
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Polyploidy
Genetic Markers
Microsatellites
Poliploidia
Marcadores Genéticos
Mimosa
Microsatélites
High Throughput Sequencing
SSR Development
SSR Transferability
Secuenciación de Alto Rendimiento
Desarrollo SSR
Transferibilidad de la SSR
topic Polyploidy
Genetic Markers
Microsatellites
Poliploidia
Marcadores Genéticos
Mimosa
Microsatélites
High Throughput Sequencing
SSR Development
SSR Transferability
Secuenciación de Alto Rendimiento
Desarrollo SSR
Transferibilidad de la SSR
dc.description.none.fl_txt_mv Mimosa L. is a megadiverse genus where lower rank classification is challenging due to widespread morphological similarities. M. subser. Obstrigosae includes 12 species with different ploidy levels. Morphological boundaries between them are defined by a few traits influenced by the environment. The extreme case is displayed by M. tandilensis and M. ramulosa which are solely defined by differences in plant habit, a trait poorly documented in herbaria. To aid species delimitation and taxonomic resolution in M. subser. Obstrigosae, we intended to develop new microsatellite markers. A ddRAD library was constructed from one individual of each M. tandilensis and M. ramulosa species. NGS derived reads were bioinformatically analysed for SSR mining. In order to avoid other sources of variation rather than the intended allelic variants, manual curation was performed. The applied selection criteria retained 72 loci from 495 candidates. Over 22 primer pairs tested, 15 polymorphic SSR were successfully amplified in a 22 individual panel test. Transferability to other species with varying phylogenetic relatedness was successful. A total of 239 variable characters (alleles), scored as presence-absence matrix, allowed to recognize species membership among 30 individuals belonging to four species of M. subser. Obstrigosae; M. adpressa and M. obstrigosa constitute two clear groups, contrarily to M. tandilensis and M. ramulosa that grouped together in several clusters. This pattern supports the hypothesis that the two latter perform a taxonomic complex, coinciding with conflicts to distinguish them by means of morphology. These results suggest that the 15 loci selected are suitable for clarifying species delimitation within M. subser. Obstrigosae. In sum, SSR development based on NGS sequencing and the selection criteria contributed herein provide a valuable tool for the molecular characterization of Mimosa beyond subseries Obstrigosae and may aid SSR development in other polyploid species.
Instituto de Recursos Biológicos
Fil: Calderón, Franco. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gilszlak, Jazmín. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; Argentina
Fil: Gutiérrez, Angela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ciencias Exactas y Naturales; Argentina
Fil: Fortunato, Reneé H. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina. Academia Nacional de Ciencias Exactas, Físicas y Naturales (IBODA-ANCEFN/CONICET). Instituto de Botánica Darwinion; Argentina
Fil: Lía, Verónica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina
Fil: Morales, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Escuela Superior de Ingeniería, Informática y Ciencias Agroalimentarias; Argentina
description Mimosa L. is a megadiverse genus where lower rank classification is challenging due to widespread morphological similarities. M. subser. Obstrigosae includes 12 species with different ploidy levels. Morphological boundaries between them are defined by a few traits influenced by the environment. The extreme case is displayed by M. tandilensis and M. ramulosa which are solely defined by differences in plant habit, a trait poorly documented in herbaria. To aid species delimitation and taxonomic resolution in M. subser. Obstrigosae, we intended to develop new microsatellite markers. A ddRAD library was constructed from one individual of each M. tandilensis and M. ramulosa species. NGS derived reads were bioinformatically analysed for SSR mining. In order to avoid other sources of variation rather than the intended allelic variants, manual curation was performed. The applied selection criteria retained 72 loci from 495 candidates. Over 22 primer pairs tested, 15 polymorphic SSR were successfully amplified in a 22 individual panel test. Transferability to other species with varying phylogenetic relatedness was successful. A total of 239 variable characters (alleles), scored as presence-absence matrix, allowed to recognize species membership among 30 individuals belonging to four species of M. subser. Obstrigosae; M. adpressa and M. obstrigosa constitute two clear groups, contrarily to M. tandilensis and M. ramulosa that grouped together in several clusters. This pattern supports the hypothesis that the two latter perform a taxonomic complex, coinciding with conflicts to distinguish them by means of morphology. These results suggest that the 15 loci selected are suitable for clarifying species delimitation within M. subser. Obstrigosae. In sum, SSR development based on NGS sequencing and the selection criteria contributed herein provide a valuable tool for the molecular characterization of Mimosa beyond subseries Obstrigosae and may aid SSR development in other polyploid species.
publishDate 2024
dc.date.none.fl_str_mv 2024-12-26T11:37:46Z
2024-12-26T11:37:46Z
2024-09-23
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/20.500.12123/20750
https://www.tandfonline.com/doi/full/10.1080/14772000.2024.2383213
1477-2000
1478-0933
https://doi.org/10.1080/14772000.2024.2383213
url http://hdl.handle.net/20.500.12123/20750
https://www.tandfonline.com/doi/full/10.1080/14772000.2024.2383213
https://doi.org/10.1080/14772000.2024.2383213
identifier_str_mv 1477-2000
1478-0933
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PD-E2-I038-002, Evaluación, monitoreo y manejo de la biodiversidad en sistemas agropecuarios y forestales
info:eu-repograntAgreement/INTA/2023-PD-L01-I087, Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Taylor and Francis
publisher.none.fl_str_mv Taylor and Francis
dc.source.none.fl_str_mv Systematics and Biodiversity 22 (1) : Article: 2383213. (2024)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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