| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Nothofagus nervosa</it> is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of <it>N. nervosa</it>, including <it>de novo</it> assembly, functional annotation, and <it>in silico</it> discovery of potential molecular markers to support population and associations genetic studies, are described.</p> <p>Results</p> <p>Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. <it>De novo</it> 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.</p> <p>Conclusions</p> <p>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, <it>N. nervosa</it>, as well as its <it>in silico</it> deduced putative functionality. The reported <it>Nothofagus</it> 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.</p>
|
|---|