Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae).

ABSTRACT: 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. • 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. • The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set

SUBMITTER: Roschanski AM 

PROVIDER: S-EPMC4105350 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature