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. E., Ding, Q., Wang, Z., Hu, J., Wang, D., Wang, F., Wang, L., Lyon, G. J., Guan, Y., Shen, Y., Evgrafov, O. V., Knowles, J. A., Thibaud-Nissen, F., Schneider, V., Yu, C. Y., Zhou, L., Eichler, E. E., So, K. F., Wang, K. (June 2016) Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun, 7. p. 12065. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

[thumbnail of Lyon_NatComm_2016.pdf]
Preview
PDF
Lyon_NatComm_2016.pdf - Published Version

Download (1MB) | Preview

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL labs > Lyon lab
Depositing User: Matt Covey
Date: 30 June 2016
Date Deposited: 01 Jul 2016 16:38
Last Modified: 10 Sep 2019 18:05
PMCID: PMC4931320
Related URLs:
URI: https://repository.cshl.edu/id/eprint/32936

Actions (login required)

Administrator's edit/view item Administrator's edit/view item