De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba
Background: Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we...
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| Format: | Artículo |
| Language: | Inglés |
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2018
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| Online Access: | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-705 http://hdl.handle.net/20.500.12123/3696 https://doi.org/10.1186/1471-2164-14-705 |
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| author | Torales, Susana Leonor Rivarola, Maximo Lisandro Pomponio, Maria Florencia Gonzalez, Sergio Alberto Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Lopez Lauenstein, Diego Verga, Anibal Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_browse | Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Gonzalez, Sergio Alberto Hopp, Horacio Esteban Lopez Lauenstein, Diego Marcucci Poltri, Susana Noemi Paniego, Norma Beatriz Pomponio, Maria Florencia Rivarola, Maximo Lisandro Torales, Susana Leonor Verga, Anibal |
| author_facet | Torales, Susana Leonor Rivarola, Maximo Lisandro Pomponio, Maria Florencia Gonzalez, Sergio Alberto Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Lopez Lauenstein, Diego Verga, Anibal Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_sort | Torales, Susana Leonor |
| collection | INTA Digital |
| description | Background: Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus.
Results: Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads. Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic.
Conclusions: This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data. The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics resources for P. alba functional analysis and genetics. Finally, it will also potentially contribute to the development of population-based genome studies in the genera. |
| format | Artículo |
| id | INTA3696 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| record_format | dspace |
| spelling | INTA36962019-11-01T13:05:29Z De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba Torales, Susana Leonor Rivarola, Maximo Lisandro Pomponio, Maria Florencia Gonzalez, Sergio Alberto Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Lopez Lauenstein, Diego Verga, Anibal Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi Prosopis Alba Marcadores Genéticos Secuencia Nucleotídica Genética Genetic Markers Nucleotide Sequence Genetics Marcadores Moleculares Secuencia Genética Algarrobo Background: Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus. Results: Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads. Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic. Conclusions: This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data. The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics resources for P. alba functional analysis and genetics. Finally, it will also potentially contribute to the development of population-based genome studies in the genera. 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: Pomponio, Maria Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina Fil: Lopez Lauenstein, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina Fil: Verga, Anibal. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales; 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 2018-10-24T14:52:22Z 2018-10-24T14:52:22Z 2013-10 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-705 http://hdl.handle.net/20.500.12123/3696 1471-2164 https://doi.org/10.1186/1471-2164-14-705 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 BMC Genomics 14 : 705 (2013) |
| spellingShingle | Prosopis Alba Marcadores Genéticos Secuencia Nucleotídica Genética Genetic Markers Nucleotide Sequence Genetics Marcadores Moleculares Secuencia Genética Algarrobo Torales, Susana Leonor Rivarola, Maximo Lisandro Pomponio, Maria Florencia Gonzalez, Sergio Alberto Acuña, Cintia Vanesa Fernandez, Paula Del Carmen Lopez Lauenstein, Diego Verga, Anibal Hopp, Horacio Esteban Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title | De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title_full | De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title_fullStr | De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title_full_unstemmed | De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title_short | De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| title_sort | de novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species prosopis alba |
| topic | Prosopis Alba Marcadores Genéticos Secuencia Nucleotídica Genética Genetic Markers Nucleotide Sequence Genetics Marcadores Moleculares Secuencia Genética Algarrobo |
| url | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-705 http://hdl.handle.net/20.500.12123/3696 https://doi.org/10.1186/1471-2164-14-705 |
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