Functional annotation of the animal genomes: An integrated annotation resource for the horse

Abstract

The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse.

A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome

“…Two randomly selected libraries were combined and then sequenced together on a single SMRT cell of the PacBio Sequel II system, as previously described. 11, 15 ChIP-seq data for the histone modifications evaluated in this study were sourced and analyzed from prior publications that examined the same eight tissues. 11, 21…”

“…11, 15 ChIP-seq data for the histone modifications evaluated in this study were sourced and analyzed from prior publications that examined the same eight tissues. 11, 21…”

“…This effort is bolstered by the Functional Annotation of the Animal Genome (FAANG) project, a large-scale collaborative effort aimed to identify all functional elements for animals. 9 The study of ASE in horses is enabled due to the availability of a high-quality reference genome 11 and long- and short-read sequencing technologies contributing to a more comprehensive transcriptome annotation. 11, 12 By extending the examination of ASE to the equine species using this method, we can further understand the uses of emerging next generation sequencing technologies and the mechanisms underlying tissue-specific gene regulation in the equine genome.…”

A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome

“…Two randomly selected libraries were combined and then sequenced together on a single SMRT cell of the PacBio Sequel II system, as previously described. 10,11 ChIP-seq data for the histone modi cations evaluated in this study were sourced and analyzed from prior publications that examined the same eight tissues. 11,18 Identifying Haplotypes…”

Transcriptomic signature related to poor welfare of sport horses

“…First, these two behavioural alterations, measured twice, showed weak correlations between the two periods of measurements [ 25 ]; second, the scan sampling method used, in particular for short-term behaviour such as alert posture may not be the most appropriate; third, the horse sample for each behavioural indicator is small for sPLS regressions because they were first selected for differential gene expression analyses, which may also explain the discrepancy with the data made on 45 horses when transcriptomic was combined to biochemical and microbiota data; fourth, the annotation of the horse genome is not complete which inevitably reduce the chance to obtain significant results. However, the latter is going to improve with the recent efforts made in annotating the horse genome through the Functional Annotation of the Animal Genomes (FAANG) project [ 69 ].…”