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

Authors: PURITZ, JON - University Of Rhode Island; GUO, XIMING - Rutgers University; HARE, MATT - Cornell University; HE, YAN - Rutgers University; HILLIER, LADEANA - Washington University; JIN, SHUBO - Rutgers University; LIU, MING - Rutgers University; LOTTERHOS, KATIE - Northeastern University; MINX, PAT - Washington University; MODAK, TEJASHREE - University Of Rhode Island; Proestou, Dina; RICE, EDWARD - Washington University; TOMLISON, CHAD - Washington University; WARREN, WESLEY - Washington University; WITKOP, ERIN - University Of Rhode Island; ZHAO, HONGGANG - Cornell University; GOMEZ-CHIARRI, MARTA - University Of Rhode Island

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2023
Publication Date: 4/25/2023
Citation: Puritz, J., Guo, X., Hare, M., He, Y., Hillier, L., Jin, S., Liu, M., Lotterhos, K., Minx, P., Modak, T., Proestou, D.A., Rice, E., Tomlison, C., Warren, W., Witkop, E., Zhao, H., Gomez-Chiarri, M. 2023. A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13801.
DOI: https://doi.org/10.1111/1755-0998.13801

Interpretive Summary: High-quality, annotated reference genomes provide a foundation for current and future research. Genome assembly algorithms perform best when the sequenced material is inbred with low levels of heterozygosity. Marine invertebrates are among the most heterozygous, polymorphic species, making contiguous genome assembly a challenge. Here we report post-hoc improvement of the eastern oyster, Crassostrea virginica, genome that resulted in a complete, highly contiguous, more acccurate reference assembly. The post-hoc improvement involved masking haplotigs, or polymorphic alleles of the same genetic locus that were incorporated in the original assembly as distinct loci. Removing haplotigs had a large impact on downstream analyses including SNP discovery, estimates of genetic diversity, and population genetic analyses. Moving forward, the haplotic masked genome should be applied to research projects aimed at supporting eastern oyster aquaculture.

Technical Abstract: Genome assembly can be challenging for species, such as terrestrial arthropods and broadcast-spawning marine invertebrates, that are characterized by high amounts of polymorphism and heterozygosity, large effective population sizes, and low levels of population differentiation. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we assembled and annotated the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly is still one of the most complete and contiguous molluscan genomes to date. We also developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream genome analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig-masking can be a powerful tool for improving genomes and we present a halpotig-masked genome assembly for the eastern oyster that will be a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry.