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

Autor: Puritz JB; Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA., Guo X; Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA., Hare M; Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA., He Y; Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA., Hillier LW; Department of Genome Sciences, University of Washington, Seattle, Washington, USA., Jin S; Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA., Liu M; Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA., Lotterhos KE; Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA., Minx P; Donald Danforth Plant Science Center, Olivette, Missouri, USA., Modak T; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA., Proestou D; USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, Rhode Island, USA., Rice ES; Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA., Tomlinson C; McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA., Warren WC; Departments of Animal Sciences and Surgery, Institute of Informatics and Data Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA., Witkop E; Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA., Zhao H; Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA., Gomez-Chiarri M; Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 Jan; Vol. 24 (1), pp. e13801. Date of Electronic Publication: 2023 Apr 25.
DOI: 10.1111/1755-0998.13801
Abstrakt: Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. 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 describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we 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 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 genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
(© 2023 John Wiley & Sons Ltd.)
Databáze: MEDLINE
Externí odkaz: