An improved pig reference genome sequence to enable pig genetics and genomics research

Area of Science:

• Genomics
• Comparative genomics
• Animal science

Background:

• The domestic pig (Sus scrofa) is a vital agricultural and biomedical model due to physiological similarities with humans.
• The previous pig reference genome (Sscrofa10.2) had limitations due to incomplete sequencing and assembly errors.

Purpose of the Study:

• To develop highly contiguous chromosome-level genome assemblies for the domestic pig.
• To provide an improved reference genome for Sus scrofa research.

Main Methods:

• Utilized long-read sequencing technologies and a whole-genome shotgun strategy.
• Generated two annotated chromosome-level assemblies: Sscrofa11.1 (Duroc female) and USMARCv1.0 (composite male).
• Annotated an additional 11 short-read assemblies.

Main Results:

• Developed two highly contiguous and accurate genome assemblies (Sscrofa11.1 and USMARCv1.0), exceeding previous versions by over 90-fold in continuity.
• These assemblies provide a comprehensive view of the pig's genetic makeup.
• The new assemblies significantly improve upon the limitations of the Sscrofa10.2 reference.

Conclusions:

• The enhanced genome assemblies offer an unprecedented resource for pig genomic research.
• Sscrofa11.1 is proposed as the new standard reference genome for the domestic pig.
• These advancements will benefit both agricultural applications and biomedical research utilizing pigs as a model.