Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa
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...
| Main Authors: | , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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Taylor and Francis
2024
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| Online Access: | 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 |
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| author | Calderón, Franco Gilslak, Jazmín Gutierrez, Ángela Verónica Fortunato, Renee Hersilia Lia, Veronica Viviana Morales, Matias |
| author_browse | Calderón, Franco Fortunato, Renee Hersilia Gilslak, Jazmín Gutierrez, Ángela Verónica Lia, Veronica Viviana Morales, Matias |
| author_facet | Calderón, Franco Gilslak, Jazmín Gutierrez, Ángela Verónica Fortunato, Renee Hersilia Lia, Veronica Viviana Morales, Matias |
| author_sort | Calderón, Franco |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA20750 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Taylor and Francis |
| publisherStr | Taylor and Francis |
| record_format | dspace |
| spelling | INTA207502024-12-26T11:59:49Z Development of SSR markers in polyploid species using ddRAD sequence data: a case study in the genus Mimosa Calderón, Franco Gilslak, Jazmín Gutierrez, Ángela Verónica Fortunato, Renee Hersilia Lia, Veronica Viviana Morales, Matias 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 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 2024-12-26T11:37:46Z 2024-12-26T11:37:46Z 2024-09-23 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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. 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) application/pdf Taylor and Francis Systematics and Biodiversity 22 (1) : Article: 2383213. (2024) |
| spellingShingle | 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 Calderón, Franco Gilslak, Jazmín Gutierrez, Ángela Verónica Fortunato, Renee Hersilia Lia, Veronica Viviana Morales, Matias 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 |
| 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_short | 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 |
| 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 |
| 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 |
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