Linked-read sequencing enables haplotype-resolved resequencing at population scale

Area of Science:

• Population genomics
• Genomic sequencing technologies
• Bioinformatics

Background:

• Accurate haplotype information is crucial for population genomic inferences like admixture and demographic history.
• Existing methods are often limited by the availability and quality of haplotype data.
• Advances in sequencing technology offer potential solutions for obtaining high-quality haplotype information.

Purpose of the Study:

• To assess the feasibility of haplotype-resolved genome resequencing at a population scale using linked-read sequencing.
• To determine the required sequencing depth for achieving adequate phasing contiguity and accuracy in bird genomes.
• To evaluate the impact of DNA input quality on phasing performance.

Main Methods:

• Investigated linked-read sequencing data from seven Oenanthe bird genomes.
• Compared downsampled sequencing depths (5× to 25×) against high-coverage data (46-68×).
• Analyzed phasing contiguity (N50, N90) and accuracy across different sequencing depths and DNA molecule lengths.

Main Results:

• Moderate sequencing depth (e.g., 15×) is sufficient for population genomic analyses, achieving ~90% genome coverage with high phasing accuracy (>99%).
• Phasing contiguity improved with increased sequencing depth and longer DNA molecule lengths.
• Higher coverages provided marginal improvements in phasing accuracy but increased contiguity.

Conclusions:

• Linked-read sequencing offers an affordable method for haplotype-resolved genome resequencing at population scale, even for large genomes.
• Moderate sequencing efforts can yield sufficient haplotype quality for diverse population genomic applications.
• Optimizing DNA input quality can enhance phasing efficiency and potentially reduce sequencing costs.