Pig assembly and gene annotation

Assembly

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).

Publications

• 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)

Other assemblies

• Sscrofa10.2 (Ensembl release 80)

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). 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 RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

• Detailed information on pig genebuild (PDF)

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.

More information

General information about this species can be found in Wikipedia.