The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

Keywords:

• pig genomes
• reference assembly
• pig
• genome annotation

Read the peer-reviewed publication(s):

(PubMed: 32543654)

Genome browser:

http://www.ensembl.org/Sus_scrofa/Info/Index

http://www.ensembl.org/Sus_scrofa/Info/Strains

https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_000003025.6

Accessions (data generated as part of this study):

BioProject: PRJNA13421
BioProject: PRJNA392765

Accessions (data referenced by this study):

BioProject: PRJNA309108
BioProject: PRJNA186497
BioProject: PRJNA144099
BioProject: PRJEB19386
BioProject: PRJEB33353
BioProject: PRJNA351265
BioProject: PRJEB9115