De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

ABSTRACT:

Background

Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, Toxoplasma gondii, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in Toxoplasma gondii is unknown. In this study, we used de novo transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in Toxoplasma and to improve the current Toxoplasma gene annotations.

Results

We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene

SUBMITTER: Hassan MA 

PROVIDER: S-EPMC3543268 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature