The Sscrofa11.1 assembly of the pig genome was produced in January 2017 by the Swine Genome Sequencing Consortium (SGSC). It consists of 20 chromosomes (1-18, X and Y) and 583 unplaced scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 48,231,277 while the scaffold N50 is 88,231,837. The pig genome sequence has been release under the term of the Toronto Statement (Nature 2009, 461: 168).
- Reference assembly: An improved pig reference genome sequence to enable pig genetics and genomics research (Warr et al. 2019)
- Pig breeds: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies (Li et al. 2017)
Sscrofa11.1 was annotated using the standard Ensembl automatic gene annotation system, incorporating RNA-Seq data and PacBio long reads provided by the SGSC. The gene annotation process was carried out using a combination of cDNA alignments, protein-to-genome alignments, PacBio long reads and RNA-seq alignments. For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs were generated via transcriptomic data where no evidence of protein homology or protein domains could be found in the transcript.
In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.
PacBio long read data set
Nine tissue samples were sequenced using the PacBio long read sequencing technology, brain, diaphragm, hypothalamus, liver, longissimus muscle, pituitary, small intestine, spleen, thymus. All sets were sequenced using 3' capping and were used to add UTR to gene models and as input source for our lincRNA discovery pipeline. Furthermore we collapsed the models created to produce a non-redundant set. We did a BLASTp of these models against UniProt proteins of vertabrate species with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). We also checked the splice junctions with the RNA-seq data set. The models with a high coding potential and with full RNA-seq support were used as input for the gene model generation.
The tissue-specific sets of aligned sequences are as follows:
|Tissue||Number of aligned sequences|
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of vertabrate species with 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 data was also used to add UTR to gene models.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Tissue||Number of gene models|
|Mesenteric lymph node||40250|
General information about this species can be found in Wikipedia.
|Assembly||Sscrofa11.1, INSDC Assembly GCA_000003025.6, Dec 2016|
|Golden Path Length||2,501,912,388|
|Annotation method||Full genebuild|
|Genebuild started||Jan 2017|
|Genebuild released||Jul 2017|
|Genebuild last updated/patched||Dec 2019|
|Non coding genes||8,979|
|Small non coding genes||2,165|
|Long non coding genes||6,797|
|Misc non coding genes||17|
|Genscan gene predictions||46,573|