GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data
GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data
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发表时间：
2018
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通讯作者：
J. Jin;Wen-bin Yu;Jun-bo Yang;Yu Song;T. Yi;De‐Zhu Li
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作者：
J. Jin;Wen-bin Yu;Jun-bo Yang;Yu Song;T. Yi;De‐Zhu Li
背景：叶绿体基因和基因组是植物遗传学和DNA条形码研究中最重要的基因组数据。随着高通量测序技术的迅速发展，低覆盖率的全基因组测序数据的获取变得非常便宜，而这些数据足以组装一个完整的叶绿体基因组。迄今为止，有许多组装过程/管道被描述为组装完整的叶绿体基因组。在这项研究中，我们报告了一个简单而快速的程序来组装一个环状叶绿体基因组使用GetOrganelle管道。调查结果：GetOrganelle流水线由四个步骤组成：1）招募质体样读段; 2）使用SPAdes从头组装; 3）过滤质体样重叠群;以及4）可视化和编辑从头组装图。其中，前三个步骤可以使用组合命令自动完成;第四步是可视化和评估装配体。在57个公开数据集的测试物种中，我们直接重组了47个物种的环状叶绿体基因组。八个非环状物种具有断点，这可能是由单核苷酸或双核苷酸重复序列或小读段池引起的。此外，我们成功地组装了其他903种被子植物的环状叶绿体基因组使用该管道，代表41个科，358属。结论：GetOrganelle管道是陆地植物组装圆形叶绿体基因组的有效方法，无需参考引导的支架，间隙填充或起点-终点关闭。该流水线还可以应用于使用基因组略读数据组装线粒体基因组和核核糖体DNA。
Background: Chloroplast genes and genomes are the most important genomic data for plant phylogeny and DNA barcoding. Since the rapid development of high throughput sequencing technologies, it is cheap to get the low coverage data of whole genome, which is enough to assemble a complete chloroplast genome. To date, there are many assembly processes/pipelines described to assemble a complete chloroplast genome. In this study, we reported a simple and fast procedure to assemble a circular chloroplast genome using GetOrganelle pipeline. Findings: The GetOrganelle pipeline consists of four steps: 1) recruiting plastid-like reads; 2) de novo assembly using SPAdes; 3) filtering plastid-like contigs; and 4) visualizing and editing de novo assembly graph. Of them, the first three steps can be fulfilled automatically just using a combined command; and the fourth step is to visualize and evaluate the assemblies. Of 57 tested species with public datasets, we directly reassembled the circular chloroplast genome in 47 species. The eight non-circular species having break points, which may be caused by mononucleotide or dinonucleotide repeats, or small reads pool. In addition, we successfully assembled the circular chloroplast genome for the other 903 species of angiosperms using this pipeline, representing 41 families and 358 genera. Conclusion: The GetOrganelle pipeline is an effective way for land plants to assemble the circular chloroplast genome, without needs for reference-guided scaffolding, gap filling nor start-end point closing. This pipeline can be also applied to assemble mitochondrial genomes and nuclear Ribosomal DNAs using genome skimming data.