Benchmarking of structural variant detection in the tetraploid potato genome using linked-read sequencing

It has recently been shown that structural variants (SV) can have a higher impact on gene expression variation compared to single nucleotide variants (SNV) in different plant species. Additionally, SV were associated with phenotypic variation in several crops. However, compared to the established SV detection based on short-read sequencing, less approaches were described for linked-read based SV calling. We therefore evaluated the performance of six linked-read SV callers compared to an established short-read SV caller based on simulated linked-reads in tetraploid potato. The objectives of our study were to i) compare the performance of SV callers based on linked-read sequencing to short-read sequencing, ii) examine the influence of SV type, SV length, haplotype incidence (HI), as well as sequencing coverage on the SV calling performance in the tetraploid potato genome, and iii) evaluate the accuracy of detecting insertions by linked-read compared to short-read sequencing. We observed high break point resolutions (BPR) detecting short SV and slightly lower BPR for large SV. Our observations highlighted the importance of short-read signals provided by Manta and LinkedSV to detect short SV. Manta and NAIBR performed well for detecting larger deletions, inversions, and duplications. Detected large SV were weakly influenced by the HI. Furthermore, we illustrated that large insertions can be assembled by Novel-X. Our results suggest the usage of the short-read and linked-read SV callers Manta, NAIBR, LinkedSV, and Novel-X based on at least 90x linked-read sequencing coverage to ensure the detection of a broad range of SV in the tetraploid potato genome.