Tissue resolved, gene structure refined equine transcriptome.

Area of Science:

• Genomics
• Transcriptomics
• Bioinformatics

Background:

• Accurate gene expression quantification and genetic variant analysis depend on high-quality reference transcriptomes.
• Current horse genome annotations are insufficient for precise gene expression assessment, particularly at the isoform level, and lack detailed untranslated region (UTR) usage information.

Purpose of the Study:

• To develop an improved annotation pipeline for the horse genome.
• To create a refined equine transcriptome by integrating extensive RNA-seq data.
• To enhance the accuracy and resolution of gene expression analysis and functional genomics in horses.

Main Methods:

• An annotation pipeline was developed for horse transcriptomes.
• 1.9 billion RNA-seq reads from multiple datasets were integrated.
• Four levels of transcript filtration were applied to generate multiple transcriptome versions.

Main Results:

• A new equine transcriptome was generated, integrating data from eight tissues across 59 individuals.
• The refined transcriptome features improved gene structure and isoform resolution, offering significant tissue-specific insights.
• The most comprehensive version includes 36,876 genes, 76,125 isoforms, and 6,474 novel transcriptional loci.

Conclusions:

• The developed pipeline and resulting equine transcriptomes provide superior tissue-specific resolution compared to existing resources.
• The transcriptomes are flexible and suitable for diverse downstream analyses, including gene expression and variant studies.
• Further integration of equine transcriptomes with the pipeline is encouraged to continuously improve equine genomic annotation.