De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina
The endangered Cedrela balansae C.DC. (Meliaceae) is a high-value timber species with great potential for forest plantations that inhabits the tropical forests in Northwestern Argentina.Research on this species is scarce because of the limited genetic and genomic information available. Here, we expl...
| Autores principales: | , , , , , , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Plos One
2019
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| Materias: | |
| Acceso en línea: | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203768 http://hdl.handle.net/20.500.12123/4320 https://doi.org/10.1371/journal.pone.0203768 |
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| author | Torales, Susana Leonor Rivarola, Maximo Lisandro Gonzalez, Sergio Alberto Inza, Maria Virginia Pomponio, Maria Florencia Fernandez, Paula Del Carmen Acuña, Cintia Vanesa Zelener, Noga Fornes, Luis Fernando Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_browse | Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Fornes, Luis Fernando Gonzalez, Sergio Alberto Hopp, Horacio Esteban Inza, Maria Virginia Marcucci Poltri, Susana Noemi Paniego, Norma Beatriz Pomponio, Maria Florencia Rivarola, Maximo Lisandro Torales, Susana Leonor Zelener, Noga |
| author_facet | Torales, Susana Leonor Rivarola, Maximo Lisandro Gonzalez, Sergio Alberto Inza, Maria Virginia Pomponio, Maria Florencia Fernandez, Paula Del Carmen Acuña, Cintia Vanesa Zelener, Noga Fornes, Luis Fernando Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_sort | Torales, Susana Leonor |
| collection | INTA Digital |
| description | The endangered Cedrela balansae C.DC. (Meliaceae) is a high-value timber species with great potential for forest plantations that inhabits the tropical forests in Northwestern Argentina.Research on this species is scarce because of the limited genetic and genomic information available. Here, we explored the transcriptome of C. balansae using 454 GS FLX Titanium next-generation sequencing (NGS) technology. Following de novo assembling, we identified 27,111 non-redundant unigenes longer than 200 bp, and considered these transcripts for further downstream analysis. The functional annotation was performed searching the 27,111 unigenes against the NR-Protein and the Interproscan databases. This analysis revealed 26,977 genes with homology in at least one of the Database analyzed. Furthermore, 7,774 unigenes in 142 different active biological pathways in C. balansae were identified with the KEGG database. Moreover, after in silico analyses, we detected 2,663 simple sequence repeats (SSRs) markers. A subset of 70 SSRs related to important “stress tolerance” traits based on functional annotation evidence, were selected for wet PCR-validation in C. balansae and other Cedrela species inhabiting in northwest and northeast of Argentina (C. fissilis, C. saltensis and C. angustifolia). Successful transferability was between 77% and 93% and thanks to this study, 32 polymorphic functional SSRs for all analyzed Cedrela species are now available. The gene catalog and molecular markers obtained here represent a starting point for further research, which will assist genetic breeding programs in the Cedrela genus and will contribute to identifying key populations for its preservation. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4320 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Plos One |
| publisherStr | Plos One |
| record_format | dspace |
| spelling | INTA43202019-01-23T16:47:35Z De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina Torales, Susana Leonor Rivarola, Maximo Lisandro Gonzalez, Sergio Alberto Inza, Maria Virginia Pomponio, Maria Florencia Fernandez, Paula Del Carmen Acuña, Cintia Vanesa Zelener, Noga Fornes, Luis Fernando Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi Cedrela Árboles Maderables Marcadores Genéticos Secuencia Nucleotídica Genética Bosque Primario Timber Trees Genetic Markers Nucleotide Sequence Genetics Primary Forests Cedrela balansae Marcadores Moleculares Bosques Nativos Región Noroeste, Argentina The endangered Cedrela balansae C.DC. (Meliaceae) is a high-value timber species with great potential for forest plantations that inhabits the tropical forests in Northwestern Argentina.Research on this species is scarce because of the limited genetic and genomic information available. Here, we explored the transcriptome of C. balansae using 454 GS FLX Titanium next-generation sequencing (NGS) technology. Following de novo assembling, we identified 27,111 non-redundant unigenes longer than 200 bp, and considered these transcripts for further downstream analysis. The functional annotation was performed searching the 27,111 unigenes against the NR-Protein and the Interproscan databases. This analysis revealed 26,977 genes with homology in at least one of the Database analyzed. Furthermore, 7,774 unigenes in 142 different active biological pathways in C. balansae were identified with the KEGG database. Moreover, after in silico analyses, we detected 2,663 simple sequence repeats (SSRs) markers. A subset of 70 SSRs related to important “stress tolerance” traits based on functional annotation evidence, were selected for wet PCR-validation in C. balansae and other Cedrela species inhabiting in northwest and northeast of Argentina (C. fissilis, C. saltensis and C. angustifolia). Successful transferability was between 77% and 93% and thanks to this study, 32 polymorphic functional SSRs for all analyzed Cedrela species are now available. The gene catalog and molecular markers obtained here represent a starting point for further research, which will assist genetic breeding programs in the Cedrela genus and will contribute to identifying key populations for its preservation. Instituto de Recursos Biológicos Fil: Torales, Susana Leonor. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Inza, Maria Virginia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Pomponio, Maria Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Zelener, Noga. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Fornes, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina 2019-01-23T16:45:27Z 2019-01-23T16:45:27Z 2018-12 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203768 http://hdl.handle.net/20.500.12123/4320 1932-6203 https://doi.org/10.1371/journal.pone.0203768 eng info:eu-repo/semantics/openAccess 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 Plos One PLoS ONE 13 (12) : e0203768 (December 2018) |
| spellingShingle | Cedrela Árboles Maderables Marcadores Genéticos Secuencia Nucleotídica Genética Bosque Primario Timber Trees Genetic Markers Nucleotide Sequence Genetics Primary Forests Cedrela balansae Marcadores Moleculares Bosques Nativos Región Noroeste, Argentina Torales, Susana Leonor Rivarola, Maximo Lisandro Gonzalez, Sergio Alberto Inza, Maria Virginia Pomponio, Maria Florencia Fernandez, Paula Del Carmen Acuña, Cintia Vanesa Zelener, Noga Fornes, Luis Fernando Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title | De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title_full | De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title_fullStr | De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title_full_unstemmed | De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title_short | De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina |
| title_sort | de novo transcriptome sequencing and ssr markers development for cedrela balansae c dc a native tree species of northwest argentina |
| topic | Cedrela Árboles Maderables Marcadores Genéticos Secuencia Nucleotídica Genética Bosque Primario Timber Trees Genetic Markers Nucleotide Sequence Genetics Primary Forests Cedrela balansae Marcadores Moleculares Bosques Nativos Región Noroeste, Argentina |
| url | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203768 http://hdl.handle.net/20.500.12123/4320 https://doi.org/10.1371/journal.pone.0203768 |
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