Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. Researchers from the University of California, Davis built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.
This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. The researchers utilized four levels of transcript filtration in their pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Their most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.
An outline of the workflow used to generate each version of the transcriptome
Transcriptome products are in ovals. Programs used to perform various steps are indicated in parentheses. All transcriptome versions and the pipeline scripts are publically available
These researchers have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. They encourage the integration of further equine transcriptomes with their annotation pipeline to continue and improve the equine transcriptome.
Availability – The data including the scripts for the pipeline as well as the GTF files for the transcriptome can be found at: https://github.com/dib-lab/horse_trans.