![]() ![]() Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. Using these 30 datasets (five reference genomes × three depths × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise F ST, and genome-wide distribution of F ST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. ![]() It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. ![]()
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