An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

Abstract

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background

“…The reads were aligned to the CanFam3.1 reference genome (Hoeppner et al 2014) using BWA 0.5.9 (Li and Durbin 2009). Using the Picard tool kit (http://broadinstitute.github.io/picard/), the duplicate reads were marked, and the data were sorted.…”

“…The filtered mutation file, along with the original BAM files and Ensembl's dog annotation v.75 (Hoeppner et al 2014) were run through Genome MuSiC 0.4 (Dees et al 2012) to produce a list of significantly mutated genes. Default settings were used, except if multiple mutations were seen in a gene in one individual, they were counted as one ("merge concurrent" option).…”

Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy

“…SP110 is a member of the SP100/SP140 family of nuclear body proteins expressed in a variety of tissues, but most strongly in immune cells (32,41,42). It is a component of promyelocytic leukemia nuclear bodies, which form a part of the nuclear matrix and influence transcription, apoptosis, senescence, and response to DNA damage or infection (43).…”

Golden Retriever dogs with neuronal ceroid lipofuscinosis have a two-base-pair deletion and frameshift in CLN5

“…The adapter sequences were trimmed from the sequence reads with custom Perl scripts and the adapter-trimmed reads were error corrected using MaSuRCA v1.9.5 software [32]. NextGENe software (SoftGenetics) was used to align the error corrected reads to the CanFam3.1 reference genome assembly [33]. The NextGENe Viewer application was used to manually scan the alignment across all coding regions of the 13 candidate genes previously associated with human NCL (Table 1) and to identify sequence variants (differences between the affected Golden Retriever genome sequence and the CanFam3.1 reference sequence).…”