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

TitleLong-read sequencing and de novo assembly of a Chinese genome
Authors
Issue Date2016
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ncomms/index.html
Citation
Nature Communications, 2016, v. 7, p. article no. 12065 How to Cite?
AbstractShort-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 39.3Mb N-bases), together with 206Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8Mb of HX1-specific sequences, including 4.1Mb 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.
Persistent Identifierhttp://hdl.handle.net/10722/230569
ISSN
2015 Impact Factor: 11.329
2015 SCImago Journal Rankings: 6.539

 

DC FieldValueLanguage
dc.contributor.authorShi, L-
dc.contributor.authorGuo, Y-
dc.contributor.authorDong, C-
dc.contributor.authorHuddleaton, J-
dc.contributor.authorYang, H-
dc.contributor.authorHan, X-
dc.contributor.authorFu, A-
dc.contributor.authorLi, Q-
dc.contributor.authorLi, N-
dc.contributor.authorGong, S-
dc.contributor.authorLintner, K. E.-
dc.contributor.authorDing, Q-
dc.contributor.authorWang, Z-
dc.contributor.authorHu, J-
dc.contributor.authorWang, D-
dc.contributor.authorWang, F-
dc.contributor.authorWang, L-
dc.contributor.authorLyon, G. J.-
dc.contributor.authorGuan, Y-
dc.contributor.authorShen, Y-
dc.contributor.authorEvgrafov, O. V.-
dc.contributor.authorKnowles, J. A.-
dc.contributor.authorThibaud-Nissen, F-
dc.contributor.authorSchneider, V-
dc.contributor.authorYu, CY-
dc.contributor.authorZhou, L-
dc.contributor.authorEichler, E. E.-
dc.contributor.authorSo, KF-
dc.contributor.authorWang, K-
dc.date.accessioned2016-08-23T14:17:48Z-
dc.date.available2016-08-23T14:17:48Z-
dc.date.issued2016-
dc.identifier.citationNature Communications, 2016, v. 7, p. article no. 12065-
dc.identifier.issn2041-1723-
dc.identifier.urihttp://hdl.handle.net/10722/230569-
dc.description.abstractShort-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 39.3Mb N-bases), together with 206Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8Mb of HX1-specific sequences, including 4.1Mb 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.-
dc.languageeng-
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ncomms/index.html-
dc.relation.ispartofNature Communications-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleLong-read sequencing and de novo assembly of a Chinese genome-
dc.typeArticle-
dc.identifier.emailSo, KF: hrmaskf@hku.hk-
dc.identifier.authoritySo, KF=rp00329-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1038/ncomms12065-
dc.identifier.hkuros261420-
dc.identifier.volume7-
dc.identifier.spagearticle no. 12065-
dc.identifier.epagearticle no. 12065-
dc.publisher.placeUnited Kingdom-

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