title: Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery.
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.
authors: Instituto de RecursosBiológicos, IRB, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), Castelar, Argentina. storales@cnia.inta.gov.ar
authors: Susana L
authors: SL
authors: Torales
authors: Máximo
authors: M
authors: Rivarola
authors: María F
authors: MF
authors: Pomponio
authors: Paula
authors: P
authors: Fernández
authors: Cintia V
authors: CV
authors: Acuña
authors: Paula
authors: P
authors: Marchelli
authors: Sergio
authors: S
authors: Gonzalez
authors: María M
authors: MM
authors: Azpilicueta
authors: Horacio Esteban
authors: HE
authors: Hopp
authors: Leonardo A
authors: LA
authors: Gallo
authors: Norma B
authors: NB
authors: Paniego
authors: Susana N Marcucci
authors: SN
authors: Poltri
mesh_terms: D001118:Argentina; D029964:Fagus / Q000235:genetics*; D015723:Gene Library; D005819:Genetic Markers; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D018749:RNA, Plant