The sheep (Ovis aries) genome was produced by the International Sheep Genome Consortium (ISGC). A single Texel ewe and a single Texel ram were sequenced using Illumina technology. The assembly is based on the Texel ewe data set. The Texel ram data set and Roche 454 reads from the previous assembly v1.0 (ACIV000000000) were used to fill in the gaps. 39,042 SNP markers and Ovine SNP50 genotyping linkage data were used to check scaffold integrity and to anchor scaffolds and super-scaffolds to chromosomes.
The assembly comprises 5,697 toplevel sequences from 130,765 contigs, 27 chromosomes (including the X chromosome). The N50 of the contigs is 40.4 kb and the N50 of the scaffolds is 100.1 Mb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000298735.1
The gene set was built using a mixed approach. The similarity pipeline was used to generate 66,797 models from orthologous vertebrate proteins from UniProtKB. The RNASeq pipeline used 8.2 billion paired-end reads provided by the ISGC. The RNASeq data contains samples from a trio (ram, ewe and lamb), 7 tissue types from the reference sheep and samples from different breeds.
We pooled the tissues to avoid creating too many fragmented models. Using the RNASeq pipeline, we created 19,604 models from the pooled set. When a pooled model was missing but we had a consensus within the tissues models, the consensus model was added to the pooled set, which brought the number of RNASeq models up to 25,832. By combining the orthologous set, the RNASeq set and our ncRNA pipeline we built the final gene set: 20,921 protein coding gene models, 291 pseudogenes and 3,985 short non-coding RNA.
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNASeq pipeline. We did a BLASTp of these models against UniProt proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Tissue||Number of gene models|
|Ewe kidney medulla||8350|
|Ewe adrenal gland||8447|
|Ewe alveolar macrophages||7747|
|Ewe corpus luteum||8096|
|Ewe heart ventricle||7256|
|Ewe lymph node mesenteric||8340|
|Ewe mammary gland||9466|
|Ewe muscle biceps||7650|
|Ewe muscle long dorsal||7185|
|Ewe peyers patch||9227|
|Ewe placenta membranes||7703|
|Ewe skin side||8795|
|Ewe thyroid gland||8167|
|Lamb adrenal gland||7813|
|Lamb kidney cortex||8416|
|Lamb kidney medulla||9115|
|Lamb lymph node mesenteric||8315|
|Lamb lymph node prescapular||8913|
|Lamb mammary gland||9924|
|Lamb muscle biceps||7633|
|Lamb muscle long dorsal||7155|
|Lamb ovarian follicles||8026|
|Lamb peyers patch||9758|
|Lamb pituitary gland||8702|
|Lamb skin back||8629|
|Lamb thyroid gland||8307|
|Ram kidney cortex||8398|
|Ram kidney medulla||8754|
|Ram abomasum mucosa||9003|
|Ram adrenal gland||8116|
|Ram alveolar macrophages||7676|
|Ram brain stem||9277|
|Ram lymph node mesenteric||7857|
|Ram lymph node prescapular||7018|
|Ram muscle biceps||6392|
|Ram muscle long dorsal||6073|
|Ram pituitary gland||8627|
|Ram skin back||8631|
|Ram testes epididymis||8805|
|Ram thyroid gland||7817|
|Reference white adipose||6755|
General information about this species can be found in Wikipedia.
|Assembly||Oar_v3.1, INSDC Assembly GCA_000298735.1, Aug 2012|
|Golden Path Length|
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
|Genebuild method||Mixed strategy build|
|Genebuild started||Dec 2012|
|Genebuild released||Dec 2013|
|Genebuild last updated/patched||Dec 2013|
Genes and/or transcript that contains an open reading frame (ORF).
|Small non coding genes|
Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.||27,099|
|Genscan gene predictions||43,449|