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

ABSTRACT: UNLABELLED: 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.

SUBMITTER: Roschanski AM

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

REPOSITORIES: biostudies-literature

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

Roschanski Anna M AM Fady Bruno B Ziegenhagen Birgit B Liepelt Sascha S

Applications in plant sciences 20130102 1

<h4>Unlabelled</h4><h4>Premise of the study</h4>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. •<h4>Methods and results</h4>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 ...[more]

PMID: 25202477

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

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

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