Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in Litopenaeus vannamei

The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 Litopenaeus vannamei (L. vannamei) samples at over 28x sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5x to 20x. Results showed that when the sequencing depth was below 10x, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10x accounting for approximately 69.16% of those detected at 20x. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6x. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10x is recommended for whole-genome studies and genetic mapping, while a depth of 6x is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species.