Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs. Mus musculus

Although the next generation sequencing platform-based single-cell genome sequencing of individual gametes was demonstrated, these methods generate short-read sequencing data, limiting their ability to study more genome diversity and instability in gametes. To overcome these limitations, we developed a long read based single-sperm genome sequencing method. Benefitting from long-read sequencing, our method can not only accurately identify crossover events and chromosomal aneuploidies in single sperms, but also efficiently detect structural variations (SVs) within individual sperm cells. More importantly, no need the help of parental genome information, in addition to heterozygous SNPs, our method could accurately de novo phase the heterozygous SVs from male individuals at whole chromosome scale with the phasing accuracy up to 98%. Besides, the repeat expansions of haplotype-resolved STRs/VNTRs in single sperm cell could also be reliably deduced. Our method provides a new chance for studying haplotype-related genetics in mammals.