Reference genome bias in light of species-specific chromosomal reorganization and translocations

作者：Marius F. Maurstad, Siv Nam Khang Hoff, José Cerca, Mark Ravinet, Ian Bradbury, Kjetill S. Jakobsen, Kim Præbel, Sissel Jentoft · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2024 · DOI：10.1101/2024.06.28.599671 · 被引用次数：10 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Disease Resistance and Genetics

Summary Whole-genome sequencing efforts has during the past decade unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling, can lead to errors and/or biases in the datasets generated for downstream analyses. Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod ( Arctogadus glacialis ), polar cod ( Boreogadus saida ), and Atlantic cod ( Gadus morhua ) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20x coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts population genetic statistics, including individual mapping depth, heterozygosity levels, and cross-species comparisons of nucleotide diversity (π) and genetic divergence (D XY ). Further, it became evident that using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that several of the detected species-specific inversions were split into multiple genomic regions when mapped towards a heterospecific reference. Inaccurate ...