Long-read sequencing and de novo assembly of a Chinese genome.
Long-read sequencing and de novo assembly of a Chinese genome.
复制标题
中国基因组的长读长测序和从头组装
DOI：
10.1038/ncomms12065
复制
发表时间：
2016-06-30
影响因子：
16.6
通讯作者：
Wang K
中科院分区：
文献类型：
--
作者：
Shi L;Guo Y;Dong C;Huddleston J;Yang H;Han X;Fu A;Li Q;Li N;Gong S;Lintner KE;Ding Q;Wang Z;Hu J;Wang D;Wang F;Wang L;Lyon GJ;Guan Y;Shen Y;Evgrafov OV;Knowles JA;Thibaud-Nissen F;Schneider V;Yu CY;Zhou L;Eichler EE;So KF;Wang K
短读测序已经使得能够从头组装几个单独的人类基因组，但在表征重复元件方面具有固有的局限性。在这里，我们通过单分子实时（SMRT）长读段测序对中国个体HX 1进行测序，通过NanoChannel阵列构建物理图谱，并生成2.93 Gb（重叠群N50：8.3 Mb，支架N50：22.0 Mb，包括39.3 Mb N-碱基）的从头组装，以及206 Mb的替代单倍型。该组装完全或部分填充参考基因组GRCh 38中的274个（28.4%）N-缺口。与GRCh 38的比较揭示了12.8 Mb的HX 1特异性序列，包括4.1 Mb的先前报道的亚洲基因组中不存在的序列。此外，转录组的长读段测序揭示了GENCODE中未注释且被短读段RNA-Seq遗漏的新剪接基因。我们的研究结果表明，改善基因组功能变异的表征可能需要使用一系列的基因组技术在不同的人群。
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.