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

被引：0

作者：

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

Francoise Thibaud-Nissen

Valerie Schneider

Chack-Yung Yu

Libing Zhou

Evan E. Eichler

Kwok-Fai So

Kai Wang

机构：

[1] Guangdong-Hongkong-Macau Institute of CNS Regeneration,Department of Genome Sciences

[2] Jinan University,Department of Pediatrics

[3] Ministry of Education Joint International Research Laboratory of CNS Regeneration,Department of Pediatrics, Department of Molecular and Human Genetics

[4] Jinan University,Departments of Systems Biology and Biomedical Informatics

[5] Co-innovation Center of Neuroregeneration,Department of Psychiatry & Behavioral Sciences

[6] Nantong University,Department of Ophthalmology

[7] Zilkha Neurogenetic Institute,undefined

[8] University of Southern California,undefined

[9] Howard Hughes Medical Institute,undefined

[10] University of Washington,undefined

[11] Genetic,undefined

[12] Molecular,undefined

[13] and Cellular Biology Program,undefined

[14] Keck School of Medicine,undefined

[15] University of Southern California,undefined

[16] Wuhan Institute of Biotechnology,undefined

[17] The Ohio State University,undefined

[18] and The Research Institute at Nationwide Children's Hospital,undefined

[19] Nextomics Biosciences,undefined

[20] School of Chemical Engineering and Pharmacy,undefined

[21] Wuhan Institute of Technology,undefined

[22] Center for Tissue Engineering and Regenerative Medicine,undefined

[23] Union Hospital,undefined

[24] Huazhong University of Science and Technology,undefined

[25] Stanley Institute for Cognitive Genomics,undefined

[26] Cold Spring Harbor Laboratory,undefined

[27] USDA/ARS Children's Nutrition Research Center,undefined

[28] Baylor College of Medicine,undefined

[29] Columbia University,undefined

[30] Keck School of Medicine,undefined

[31] University of Southern California,undefined

[32] National Center for Biotechnology Information,undefined

[33] U.S. National Library of Medicine,undefined

[34] The University of Hong Kong,undefined

[35] State Key Laboratory of Brain and Cognitive Sciences,undefined

[36] The University of Hong Kong,undefined

来源：

Nature Communications | / 7卷

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摘要：

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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