Journal
ECOLOGY AND EVOLUTION
Volume 12, Issue 12, Pages -Publisher
WILEY
DOI: 10.1002/ece3.9583
Keywords
aquatic insects; de novo genomes; population genomics; reference genomes; sequencing depth; whole genome resequencing
Categories
Funding
- Deutsche Forschungsgemeinschaft [AF 1117/1-2, PA 1617/2-1, PA 1617/2-2]
- LOEWE -Landes-Offensive zur Entwicklung Wissenschaftlich-okonomischer Exzellenz of Hesse's Ministry of Higher Education, Research and the Arts
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Whole genome sequencing for generating SNP data is commonly used in population genetic studies. This study investigates the effect of reference genome and sequencing depth on downstream analyses in caddisfly species. The results show that distantly related reference genomes and lower sequencing depth lead to decreased resolution, but a more closely related reference genome can compensate for the defects caused by low depth. Therefore, population genetic studies can benefit from closely related reference genomes, and a trade-off between reference genome relatedness and sequencing depth should be considered for cost-efficient strategies.
Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. 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. 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 (3.5x, 7.5x and 12x) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes x three depths x 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. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. 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. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.
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