Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers t...
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todo:paper_14712164_v13_n1_p_Torales2023-10-03T16:17:46Z Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery Torales, S.L. Rivarola, M. Pomponio, M.F. Fernández, P. Acuña, C.V. Marchelli, P. Gonzalez, S. Azpilicueta, M.M. Hopp, H.E. Gallo, L.A. Paniego, N.B. Poltri, S.N.M. de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described.Results: Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic.Conclusions: This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. © 2012 Torales et al.; licensee BioMed Central Ltd. Fil:Rivarola, M. 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:Acuña, C.V. 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14712164_v13_n1_p_Torales |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa |
| spellingShingle |
de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa Torales, S.L. Rivarola, M. Pomponio, M.F. Fernández, P. Acuña, C.V. Marchelli, P. Gonzalez, S. Azpilicueta, M.M. Hopp, H.E. Gallo, L.A. Paniego, N.B. Poltri, S.N.M. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| topic_facet |
de novo transcriptome assembly Forest genomics Functional annotation Nothofagaceae Pyrosequencing SSRs complementary DNA molecular marker transcriptome article beech DNA library ecology genetic association genetic conservation genetic transcription molecular evolution nonhuman Nothofagus nervosa nucleotide sequence plant genetics plant leaf population dynamics pyrosequencing RNA sequence simple sequence repeat species differentiation species diversity unindexed sequence Argentina Fagus Gene Library Genetic Markers Microsatellite Repeats Molecular Sequence Annotation RNA, Plant Sequence Analysis, DNA Transcriptome Fagus Nothofagaceae Nothofagus Nothofagus alpina Nothofagus nervosa |
| description |
Background: Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described.Results: Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic.Conclusions: This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. © 2012 Torales et al.; licensee BioMed Central Ltd. |
| format |
JOUR |
| author |
Torales, S.L. Rivarola, M. Pomponio, M.F. Fernández, P. Acuña, C.V. Marchelli, P. Gonzalez, S. Azpilicueta, M.M. Hopp, H.E. Gallo, L.A. Paniego, N.B. Poltri, S.N.M. |
| author_facet |
Torales, S.L. Rivarola, M. Pomponio, M.F. Fernández, P. Acuña, C.V. Marchelli, P. Gonzalez, S. Azpilicueta, M.M. Hopp, H.E. Gallo, L.A. Paniego, N.B. Poltri, S.N.M. |
| author_sort |
Torales, S.L. |
| title |
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| title_short |
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| title_full |
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| title_fullStr |
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| title_full_unstemmed |
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery |
| title_sort |
transcriptome survey of patagonian southern beech nothofagus nervosa (= n. alpina): assembly, annotation and molecular marker discovery |
| url |
http://hdl.handle.net/20.500.12110/paper_14712164_v13_n1_p_Torales |
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