Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.
Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.
复制标题
DOI：
10.1371/journal.pone.0055864
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Xiao M
中科院分区：
文献类型：
--
作者：
Hastie AR;Dong L;Smith A;Finklestein J;Lam ET;Huo N;Cao H;Kwok PY;Deal KR;Dvorak J;Luo MC;Gu Y;Xiao M
下一代测序（NGS）技术已经实现了高通量和低成本的序列数据生成;然而，从头基因组组装仍然是一个巨大的挑战，特别是对于大基因组。NGS短读段通常不足以产生跨越重复序列的大重叠群并促进明确的组装。植物基因组因含有大量重复元件而臭名昭著，这与巨大的基因组大小相结合，使得迄今为止这些大型复杂基因组的精确组装变得困难。使用双色基因组作图的平铺细菌人工染色体（BAC）克隆的纳米通道阵列，我们完成了高置信度组装的2.1 Mb，高度重复的区域在大型和复杂的基因组的节节麦，D-基因组供体的六倍体小麦（小麦）。基因组作图是基于对单个DNA分子上数百个碱基长度的序列基序的直接可视化。以基因组图谱为支架，我们锚定了未放置的序列重叠群，验证了最初的组装草案，并解决了错误组装的情况，其中一些涉及长度<2 kb的重叠群，从而将组装完成率从75%大幅提高到95%。
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.
登录
查看更多内容
影响因子：
5.6
作者：
Leroy P;Guilhot N;Sakai H;Bernard A;Choulet F;Theil S;Reboux S;Amano N;Flutre T;Pelegrin C;Ohyanagi H;Seidel M;Giacomoni F;Reichstadt M;Alaux M;Gicquello E;Legeai F;Cerutti L;Numa H;Tanaka T;Mayer K;Itoh T;Quesneville H;Feuillet C
通讯作者：
Feuillet C
影响因子：
7.2
作者：
Hernandez, Pilar;Martis, Mihaela;Mayer, Klaus F. X.
通讯作者：
Mayer, Klaus F. X.
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
56.9
作者：
SCHWARTZ, DC;LI, XJ;WANG, YK
通讯作者：
WANG, YK
影响因子：
46.9
作者：
通讯作者：
--