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

Lingling Shi | Zendy; Yunfei Guo | Zendy; Chengliang Dong | Zendy; John Huddleston | Zendy; Hui Yang | Zendy; Xiaolu Han | Zendy; Aisi Fu | Zendy; Quan Li | Zendy; Na Li | Zendy; Siyi Gong | Zendy; Katherine E. Lintner | Zendy; Qiong Ding | Zendy; Zou Wang | Zendy; Jiang Hu | Zendy; Depeng Wang | Zendy; Feng Wang | Zendy; Lin Wang | Zendy; Gholson J. Lyon | Zendy; Yongtao Guan | Zendy; Yufeng Shen | Zendy; Oleg V. Evgrafov | Zendy; James A. Knowles | Zendy; Françoise ThibaudNissen | Zendy; Valérie Schneider | Zendy; C. Yung Yu | Zendy; Libing Zhou | Zendy; Evan E. Eichler | Zendy; KwokFai So | Zendy; Kai Wang | Zendy

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

Author(s) -

Lingling Shi,

Yunfei Guo,

Chengliang Dong,

John Huddleston,

Hui Yang,

Xiaolu Han,

Aisi Fu,

Quan Li,

Na Li,

Siyi Gong,

Katherine E. Lintner,

Qiong Ding,

Zou Wang,

Jiang Hu,

Depeng Wang,

Feng Wang,

Lin Wang,

Gholson J. Lyon,

Yongtao Guan,

Yufeng Shen,

Oleg V. Evgrafov,

James A. Knowles,

Françoise ThibaudNissen,

Valérie Schneider,

C. Yung Yu,

Libing Zhou,

Evan E. Eichler,

KwokFai So,

Kai Wang

Publication year - 2016

Publication title -

nature communications

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 5.559

H-Index - 365

ISSN - 2041-1723

DOI - 10.1038/ncomms12065

Subject(s) - contig , sequence assembly , genome , computational biology , biology , de novo transcriptome assembly , hybrid genome assembly , human genome , reference genome , dna sequencing , genomics , genetics , transcriptome , gene , gene expression

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.

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