Annotation and re‐sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae)1. (2nd January 2013)

• Record Type: Journal Article
• Authors: Roschanski, Anna M.; Fady, Bruno; Ziegenhagen, Birgit; Liepelt, Sascha
• Is Part Of: Applications in plant sciences. Volume 1:Number 1(2013)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2013-01-02
• Subjects: Abies alba -- adaptation -- annotation -- candidate genes -- de novo sequencing -- Pinaceae; Plants -- Periodicals; Plant physiology -- Periodicals; Plant Physiological Phenomena; Plant physiology; Plants; Periodicals; Periodicals; Fulltext; Internet Resources; Periodicals; 580
• DOI: 10.3732/apps.1200179
• Languages: English
• ISSNs: 2168-0450

Abstract

Abstract : Premise of the study: 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 . Methods and 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 .