Ryan 发表于 2016-7-1 20:18

转: 基于长读长测序的中国人基因组拼接完成

本帖最后由 Ryan 于 2016-7-1 20:20 编辑

Nature Communications | doi:10.1038/ncomms12065

Long-read sequencing and de novo assembly of a Chinese genome
Lingling Shi,...

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.

全文:http://www.nature.com/ncomms/2016/160630/ncomms12065/full/ncomms12065.html

Ryan 发表于 2016-7-1 20:20

本帖最后由 Ryan 于 2016-7-1 20:24 编辑

http://www.seq.cn/portal.php?mod=view&aid=20149

http://www.bio360.net/news/show/27322.html


6月30日,Nature communication发表了由暨南大学等单位的完成的基于长读长测序技术的中国人基因组的重头拼接工作。虽然通过短读长测序已完成了多个人类基因组的de novo拼接工作,但是对于基因组中的重复序列的拼接仍存在技术限制。暨南大学等机构的研究人员利用单分子实时测序技术(SMRT)对代号名为“HX1”的中国人基因组进行长读长测序。并通过纳米通道array构建物理图谱,获得了大小为2.93Gb (contig N50: 8.3Mb, scaffold N50: 22.0Mb, including 39.3MbN-bases)的基因组,以及206Mb alternative haplotypes。该研究对人类参考基因组GRCh38进行274个N-gap修补。与GRCh38相比,HX1中有12.8Mb的特有序列,其中包括4.1 Mb之前没有被报道过的亚洲人基因序列。此外,利用长读长测序发现了可变剪切产生的新基因,这些基因在GENCODE数据库里尚无注释,如果利用短读长RNA测序无法发现这些可变剪切位点。该研究结果暗示,如果想要更深入了解基因组功能变化需要针对不同人群使用一系列基因技术。

imvivi001 发表于 2016-7-1 21:01

总算取得一定的进步,基因科技对国家和民族未来至关重要,中国人,加油!

一统浆糊 发表于 2016-7-2 00:37

不错。这个序列出来后对短序列测序的拼接也有帮助。等于一下子把所有的测序质量都提高了。
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