Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.
复制标题
直接从基因组下一代测序读取中重建线粒体基因组 - 一种诱饵和迭代映射方法。
DOI：
10.1093/nar/gkt371
复制
发表时间：
2013-07
影响因子：
14.9
通讯作者：
Chevreux B
中科院分区：
文献类型：
--
作者：
Hahn C;Bachmann L;Chevreux B
我们提出了一种直接从下一代测序（NGS）数据-线粒体诱饵和迭代作图（MITObim）重建非模式生物完整线粒体基因组的计算机方法。即使只有（i）远亲线粒体基因组或（ii）线粒体条形码序列分别可用作起始参考序列或种子，该方法也很简单。我们证明了该方法的效率，在案例研究中使用真实的NGS数据集的两个单殖吸虫体外寄生虫种三代虫thymalli和三代虫derjavinoides，包括其各自的硬骨鱼主机欧洲灰（Thymallus thymallus）和虹鳟鱼（虹鳟）。MITObim在准确性、运行时间和内存要求方面上级现有工具，并且使用标准台式计算机在<24小时内从总基因组DNA衍生的NGS数据集完全自动恢复线粒体基因组，准确率超过99.5%。该方法克服了传统策略的局限性，获得线粒体基因组的物种很少或没有线粒体序列信息在手，并代表了一个快速，高效的替代在硅片上的传统策略依赖于初始的远程PCR。我们还证明了使用模拟数据的宏基因组/合并数据集的MITObim的适用性。MITObim是一个易于使用的工具，即使是对生物信息学经验有限的生物学家也是如此。该软件在https://github.com/chrishah/MITObim上以MIT许可证下的开源管道提供。
We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
登录
查看更多内容
DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
3.7
作者：
Edwards CJ;Magee DA;Park SD;McGettigan PA;Lohan AJ;Murphy A;Finlay EK;Shapiro B;Chamberlain AT;Richards MB;Bradley DG;Loftus BJ;MacHugh DE
通讯作者：
MacHugh DE
影响因子：
3.7
作者：
Haiminen N;Kuhn DN;Parida L;Rigoutsos I
通讯作者：
Rigoutsos I
DOI：
10.1073/pnas.0914266107
发表时间：
2010-03-16
影响因子：
11.1
作者：
Lindqvist, Charlotte;Schuster, Stephan C.;Wiig, Oystein
通讯作者：
Wiig, Oystein
影响因子：
2.8
作者：
Liu, Guo-Hua;Lin, Rui-Qing;Zhu, Xing-Quan
通讯作者：
Zhu, Xing-Quan