Abstract
BackgroundThe 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.ResultsWe present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2.ConclusionsThese 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.
Highlights
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
In farmed animal species such as the domestic pig (Sus scrofa, NCBI:txid9823) genome sequences have been integral to the discovery of molecular genetic variants and the development of single-nucleotide polymorphism (SNP) chips [1] and enabled efforts to dissect the genetic control of complex traits, such as growth, feed conversion, body composition, reproduction, behaviour, and responses to infectious diseases [2]
Two individual pigs were sequenced independently: (i) TJ Tabasco (Duroc 2–14), i.e., the sow that was the primary source of DNA for the published draft genome sequence (Sscrofa10.2) [13] and (ii) MARC1423004, which was a crossbred barrow from a composite population at the United States Department of Agriculture (USDA) Meat Animal Research Center
Summary
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. Results: We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. A high quality, richly annotated genome sequence is essential when using gene editing technologies to engineer improved animal models for research or as sources of cells and tissue for xenotransplantation and potentially for improved productivity [7, 8]
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