De Novo Assembly Of A Haplotype-resolved Human Genome

Human chromosomal inheritance is diploid, with each half of any given pair of homologous chromosomes inherited from one of two parents. However, no diploid human genome sequence has been de novo assembled other than that of the Human Genome Project(HGP). Here, we provide the first de novo haplotype-resolved diploid genome sequence of an Asian individual using a unique de novo assembly pipeline. Our pipeline uses fosmid pooling to generate ~614,850 fosmid clones ranging from 20 kbp-80 kbp with a mean of 36 kbp and then it was combined with whole genome shotgun strategies and next generation sequencing(NGS) technology. The assembled genome contains 5.15 Gb, with a haplotype N50 of 484 kbp. In total, we identified 3.58 M SNP, 762 k short indels(≤50 bp), 30 k long indels(Longest 37 kbp), 111 inversions(Longest 87 kb) and 168 translocations(Longest 17.8 kb). There were 22,875 SNPs, 959 indels, 21 inversions, and 20 translocations located in the exonic regions and about half of these altered the amino acid sequence. The non-synonymous variants affected 5,701 genes and 1,340 of the variants(in 1,017 genes) were predicted to be deleterious and were related to 153 currently known diseases. This haplotype-resolved genome represents the most complete genome assembly so far. Our analysis further identified previously undetected indels and novel coding sequences, and thus provides the most complete representation of an individual’s genetic variation. Application of these methods and identification of individual differences will aide in translating genotypes to phenotypes, and potentially allow more personalized medicine. Also, it might be contributed to the studies of complex genome, such as insects, sea lives.