A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference

Area of Science:

• Genomics
• Marine Biology
• Aquaculture

Background:

• High heterozygosity in species like the eastern oyster complicates genome assembly.
• This can lead to mis-assemblies and inflated genome sizes due to haplotigs.

Purpose of the Study:

• To describe the first chromosome-level genome assembly for Crassostrea virginica.
• To develop and evaluate a method for masking haplotigs in heterozygous genomes.
• To improve downstream genomic analyses.

Main Methods:

• Chromosome-level genome assembly of Crassostrea virginica.
• Development of a post hoc method to identify and mask haplotigs.
• Evaluation of the impact of haplotig masking on various genomic analyses.

Main Results:

• The Crassostrea virginica genome assembly is chromosome-level, >97% complete, with a scaffold N50 of 54 mb.
• Haplotig masking significantly impacted SNP discovery and nucleotide diversity estimates.
• Subtle but nuanced effects were observed on heterozygosity, population structure, and outlier detection.

Conclusions:

• The eastern oyster genome is a vital resource for understanding adaptation and aquaculture.
• Haplotig masking is a powerful tool for enhancing genomic inference in heterozygous species.
• An open, reproducible resource for haplotig masking is now available.