Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements, and duplication

• Published in: Genome Biology and Evolution
• Main Authors: Dallaire, Xavier, Bouchard, Raphael, Hénault, Philippe, Ulmo-Díaz, Gabriela, Normandeau, Eric, Mérot, Claire, Bernatchez, Louis, Moore, Jean-Sébastien
• Other Authors: Université Laval Québec (ULaval), Ecosystèmes, biodiversité, évolution Rennes (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement - CNRS Ecologie et Environnement (INEE-CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: heterozygosity; salmonid; whole-genome sequencing; paralog; autopolyploid; repetitive DNA; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Arctic; Atlantic salmon; Salmo salar; Salvelinus alpinus
• Online Access: https://hal.science/hal-04350851; https://hal.science/hal-04350851/document; https://hal.science/hal-04350851/file/evad229.pdf; https://doi.org/10.1093/gbe/evad229

International audience Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing data with low (1.5X) to intermediate (4.8X) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22 to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.