Long-read sequencing and de novo assembly of a Chinese genome.

Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner K, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon G, Guan Y, Shen Y, Evgrafov O, Knowles J, Thibaud-Nissen F, Schneider V, Yu C, Zhou L, Eichler E, So K, Wang K

Nature communications, 2016.

Lab members marked as bold

PDF
Shi_2016.pdf
DOI
10.1038/ncomms12065
PMID
27356984

Abstract

Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.