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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| Autores principales: | , , , , , , , , , , |
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| Formato: | Artículo publishedVersion |
| Lenguaje: | Inglés |
| Publicado: |
2013
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_14712164_v14_n1_p_Torales |
| Aporte de: |
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paperaa:paper_14712164_v14_n1_p_Torales |
|---|---|
| record_format |
dspace |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| language |
Inglés |
| orig_language_str_mv |
eng |
| topic |
Fabaceae Functional annotation Prosopis alba Pyrosequencing SNPs SSRs Transcriptome assembly molecular marker transcriptome microsatellite DNA transcriptome vegetable protein article chloroplast genome controlled study DNA determination DNA flanking region DNA sequence genome analysis microsatellite marker plant leaf Prosopis Prosopis alba pyrosequencing sequence analysis simple sequence repeat single nucleotide polymorphism transcriptomics validation process chloroplast gene frequency gene ontology genetic marker genetics high throughput sequencing metabolism molecular genetics plant gene plant leaf Fabaceae Prosopis Prosopis alba Chloroplasts Gene Frequency Gene Ontology Genes, Plant Genetic Markers High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Microsatellite Repeats Molecular Sequence Annotation Plant Leaves Plant Proteins Polymorphism, Single Nucleotide Prosopis Sequence Analysis, DNA Transcriptome |
| spellingShingle |
Fabaceae Functional annotation Prosopis alba Pyrosequencing SNPs SSRs Transcriptome assembly molecular marker transcriptome microsatellite DNA transcriptome vegetable protein article chloroplast genome controlled study DNA determination DNA flanking region DNA sequence genome analysis microsatellite marker plant leaf Prosopis Prosopis alba pyrosequencing sequence analysis simple sequence repeat single nucleotide polymorphism transcriptomics validation process chloroplast gene frequency gene ontology genetic marker genetics high throughput sequencing metabolism molecular genetics plant gene plant leaf Fabaceae Prosopis Prosopis alba Chloroplasts Gene Frequency Gene Ontology Genes, Plant Genetic Markers High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Microsatellite Repeats Molecular Sequence Annotation Plant Leaves Plant Proteins Polymorphism, Single Nucleotide Prosopis Sequence Analysis, DNA Transcriptome Torales, S.L. Rivarola, M. Pomponio, M.F. Gonzalez, S. Acuña, C.V. Fernández, P. Lauenstein, D.L. Verga, A.R. Hopp, H.E. Paniego, N.B. Poltri, S.N.M. De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba |
| topic_facet |
Fabaceae Functional annotation Prosopis alba Pyrosequencing SNPs SSRs Transcriptome assembly molecular marker transcriptome microsatellite DNA transcriptome vegetable protein article chloroplast genome controlled study DNA determination DNA flanking region DNA sequence genome analysis microsatellite marker plant leaf Prosopis Prosopis alba pyrosequencing sequence analysis simple sequence repeat single nucleotide polymorphism transcriptomics validation process chloroplast gene frequency gene ontology genetic marker genetics high throughput sequencing metabolism molecular genetics plant gene plant leaf Fabaceae Prosopis Prosopis alba Chloroplasts Gene Frequency Gene Ontology Genes, Plant Genetic Markers High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Microsatellite Repeats Molecular Sequence Annotation Plant Leaves Plant Proteins Polymorphism, Single Nucleotide Prosopis Sequence Analysis, DNA Transcriptome |
| 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. © 2013 Torales et al.; licensee BioMed Central Ltd. |
| format |
Artículo Artículo publishedVersion |
| author |
Torales, S.L. Rivarola, M. Pomponio, M.F. Gonzalez, S. Acuña, C.V. Fernández, P. Lauenstein, D.L. Verga, A.R. Hopp, H.E. Paniego, N.B. Poltri, S.N.M. |
| author_facet |
Torales, S.L. Rivarola, M. Pomponio, M.F. Gonzalez, S. Acuña, C.V. Fernández, P. Lauenstein, D.L. Verga, A.R. Hopp, H.E. Paniego, N.B. Poltri, S.N.M. |
| author_sort |
Torales, S.L. |
| 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_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_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_sort |
de novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species prosopis alba |
| publishDate |
2013 |
| url |
http://hdl.handle.net/20.500.12110/paper_14712164_v14_n1_p_Torales |
| work_keys_str_mv |
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paperaa:paper_14712164_v14_n1_p_Torales2023-06-12T16:50:25Z De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba BMC Genomics 2013;14(1) Torales, S.L. Rivarola, M. Pomponio, M.F. Gonzalez, S. Acuña, C.V. Fernández, P. Lauenstein, D.L. Verga, A.R. Hopp, H.E. Paniego, N.B. Poltri, S.N.M. Fabaceae Functional annotation Prosopis alba Pyrosequencing SNPs SSRs Transcriptome assembly molecular marker transcriptome microsatellite DNA transcriptome vegetable protein article chloroplast genome controlled study DNA determination DNA flanking region DNA sequence genome analysis microsatellite marker plant leaf Prosopis Prosopis alba pyrosequencing sequence analysis simple sequence repeat single nucleotide polymorphism transcriptomics validation process chloroplast gene frequency gene ontology genetic marker genetics high throughput sequencing metabolism molecular genetics plant gene plant leaf Fabaceae Prosopis Prosopis alba Chloroplasts Gene Frequency Gene Ontology Genes, Plant Genetic Markers High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Microsatellite Repeats Molecular Sequence Annotation Plant Leaves Plant Proteins Polymorphism, Single Nucleotide Prosopis Sequence Analysis, DNA Transcriptome 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. © 2013 Torales et al.; licensee BioMed Central Ltd. Fil:Rivarola, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Acuña, C.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Fernández, P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Poltri, S.N.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2013 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion application/pdf eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14712164_v14_n1_p_Torales |