Haplotype-resolved assembly of a pig genome using single-sperm sequencing

Area of Science:

• Genomics
• Animal Genetics
• Reproductive Biology

Background:

• Chromosome-level phased genomes are crucial for understanding genetic variation and inheritance.
• Accurate genome phasing is challenging, especially for complex genomes.
• Single gamete cell sequencing offers a unique resource for genetic studies.

Purpose of the Study:

• To develop and validate a novel haplotype assembly method for chromosome-level phased genomes.
• To investigate the utility of single-sperm sequencing for genetic mapping and trait association.
• To improve the assembly of the Y chromosome and explore its role in reproductive traits.

Main Methods:

• Employed PacBio HiFi and Hi-C sequencing on a male Landrace pig.
• Utilized single-sperm sequencing for 102 individual sperm cells.
• Developed a haplotype assembly method integrating long-read data and sperm-phased markers.

Main Results:

• Achieved higher phasing accuracy compared to methods relying solely on HiFi reads.
• Constructed a genetic map and mapped the sperm motility trait to chromosome 1 (105.40-110.70 Mb).
• Assembled 26.16 Mb of Y chromosome sequences using Y chromosome-bearing sperm data.

Conclusions:

• Presented a reliable approach for assembling chromosome-level phased genomes.
• Demonstrated the potential of sperm populations in basic biology and sperm phenotype research.
• Highlighted the value of integrating long-read and single-sperm sequencing for advanced genomic studies.