De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads.
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads.
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DOI：
10.1186/s12915-017-0473-4
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发表时间：
2018-01-11
期刊：
影响因子：
5.4
通讯作者：
Ewbank JJ
中科院分区：
文献类型：
--
作者：
Eccles D;Chandler J;Camberis M;Henrissat B;Koren S;Le Gros G;Ewbank JJ
真核基因组组装仍然是一个挑战，部分原因是复杂 DNA 重复的普遍存在。对于全中心线虫来说，这是一个特别严重的问题，因为在其基因组中发现了大量卫星 DNA 序列。这些对于大多数基因组测序方法来说都是难以接受的。同时，许多线虫是寄生虫，有些对人类健康构成严重威胁。迫切需要对动植物寄生线虫进行更好的分子表征。长读长 DNA 测序方法的出现为解析复杂的基因组带来了希望。使用巴西尼波圆线虫作为测试案例，应用改进的碱基识别算法和组装方法，我们证明了仅使用 MinION 长读长匹配当前社区标准的从头基因组组装的可行性。在此过程中，我们发现了整个巴西猪笼草基因组中重复的非常长且复杂的 DNA 序列的意外多样性，包括 tRNA 基因的大量串联重复。碱基识别和组装方法已得到充分改进，仅使用长读长即可实现大型复杂基因组的从头基因组组装。该方法具有保留单倍型变异的额外优势，因此有可能用于群体分析。本文的在线版本 (10.1186/s12915-017-0473-4) 包含补充材料，可供授权用户使用。
Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes. Using Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA sequences repeated throughout the N. brasiliensis genome, including massive tandem repeats of tRNA genes. Base-calling and assembly methods have improved sufficiently that de novo genome assembly of large complex genomes is possible using only long reads. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses. The online version of this article (10.1186/s12915-017-0473-4) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Subirana JA;Messeguer X
通讯作者：
Messeguer X
影响因子：
12.3
作者：
Koren S;Harhay GP;Smith TP;Bono JL;Harhay DM;Mcvey SD;Radune D;Bergman NH;Phillippy AM
通讯作者：
Phillippy AM
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
5.8
作者：
Simao, Felipe A.;Waterhouse, Robert M.;Zdobnov, Evgeny M.
通讯作者：
Zdobnov, Evgeny M.