An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts

Area of Science:

• Genomics
• Comparative genomics
• Transcriptomics

Background:

• The domestic dog (Canis familiaris) is a valuable model for genetic studies, but its genome annotation was limited by gaps, especially in regulatory regions.
• Previous canine genome builds hindered comprehensive gene annotation and the study of candidate genes.

Purpose of the Study:

• To present an improved canine genome build, canFam3.1, with enhanced sequence coverage.
• To comprehensively catalog expressed loci and transcript isoforms using RNA-Sequencing across multiple canine tissues.
• To identify novel protein-coding and non-coding transcripts, including long intergenic non-coding RNAs (lincRNAs), and assess their potential functions.

Main Methods:

• Assembly of an improved canine genome build (canFam3.1) incorporating novel sequence data.
• RNA-Sequencing across 10 diverse canine tissues to profile gene expression.
• Bioinformatic analysis including gene annotation, transcript isoform detection, and syntenic comparison with the human genome.
• Functional analysis of novel transcripts using shRNA in a mouse cell line.

Main Results:

• The canFam3.1 genome build covers 99.8% of the euchromatic genome, adding 85 MB of novel sequence.
• RNA-Seq data identified approximately 175,000 expressed loci, expanding transcript isoform annotations by fourfold compared to previous Ensembl annotations.
• Over 7,200 potential long intergenic non-coding RNAs (lincRNAs) were identified, with ~6,000 lacking human or mouse orthologs. Functional assays indicated regulatory roles for some novel transcripts.
• Approximately 3,000 additional protein-coding loci, expressed in dogs, were identified through syntenic comparison with the human genome.

Conclusions:

• The canFam3.1 genome build provides a significantly improved resource for canine genomics and genetic research.
• The comprehensive transcript catalog reveals a vastly expanded repertoire of canine gene expression, including numerous novel non-coding RNAs.
• Novel non-coding transcripts, particularly lincRNAs, represent a promising area for further investigation into gene regulation and function in dogs.