title: Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae).
abstract: OBJECTIVE
  We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. •
  
  
  RESULTS
  A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA. •
  
  
  CONCLUSIONS
  The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in A. alba.
authors.affiliation: University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany.
authors.forename: Anna M
authors.initials: AM
authors.lastname: Roschanski
authors.affiliation: INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Fady
authors.affiliation: University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Ziegenhagen
authors.affiliation: University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany.
authors.forename: Sascha
authors.initials: S
authors.lastname: Liepelt
keywords: Abies alba; Pinaceae; adaptation; annotation; candidate genes; de novo sequencing