Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.

ABSTRACT:

Background

Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads.

Results

Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (approximately 19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 c

SUBMITTER: Hale MC 

PROVIDER: S-EPMC2688523 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature