Artículo

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" (2012) BMC Genomics. 13(1)
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Abstract:

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.

Registro:

Documento: Artículo
Título:Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
Autor: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.
Filiación:Instituto de RecursosBiológicos, IRB, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar, B1712WAA, Argentina
Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar, B1712WAA, Argentina
EEA Bariloche, Genética Ecológica y Mejoramiento Forestal, Instituto Nacional de Tecnología Agropecuaria (INTA Bariloche), CC 277, 8400, Bariloche, Argentina
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
CONICET, Buenos Aires, Argentina
Palabras clave: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
Año:2012
Volumen:13
Número:1
DOI: http://dx.doi.org/10.1186/1471-2164-13-291
Título revista:BMC Genomics
Título revista abreviado:BMC Genomics
ISSN:14712164
CODEN:BGMEE
CAS:Genetic Markers; RNA, Plant
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712164_v13_n1_p_Torales

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Citas:

---------- APA ----------
Torales, S.L., Rivarola, M., Pomponio, M.F., Fernández, P., Acuña, C.V., Marchelli, P., Gonzalez, S.,..., Poltri, S.N.M. (2012) . Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery. BMC Genomics, 13(1).
http://dx.doi.org/10.1186/1471-2164-13-291
---------- CHICAGO ----------
Torales, S.L., Rivarola, M., Pomponio, M.F., Fernández, P., Acuña, C.V., Marchelli, P., et al. "Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery" . BMC Genomics 13, no. 1 (2012).
http://dx.doi.org/10.1186/1471-2164-13-291
---------- MLA ----------
Torales, S.L., Rivarola, M., Pomponio, M.F., Fernández, P., Acuña, C.V., Marchelli, P., et al. "Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery" . BMC Genomics, vol. 13, no. 1, 2012.
http://dx.doi.org/10.1186/1471-2164-13-291
---------- VANCOUVER ----------
Torales, S.L., Rivarola, M., Pomponio, M.F., Fernández, P., Acuña, C.V., Marchelli, P., et al. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery. BMC Genomics. 2012;13(1).
http://dx.doi.org/10.1186/1471-2164-13-291