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)
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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 |
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