ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes.
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes.
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Eztree：一种自动化管道，用于鉴定系统发育基因基因并推断出未培养的原核基因组之间的进化关系。
DOI：
10.1186/s12864-017-4327-9
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发表时间：
2018-01-19
期刊：
影响因子：
4.4
通讯作者：
Wu YW
中科院分区：
文献类型：
--
作者：
Wu YW
从后基因组样本中推断新获得的基因组的系统发育树在确定未培养微生物的身份方面非常有用。尽管16S核糖体RNA小亚基基因已被确定为推测系统发育树的金标准标记，但由于16S基因之间存在共同的区域，它们通常不能很好地组装在元基因组中。使用单拷贝标记基因来构建基因组树对于非栽培物种来说已经变得越来越流行。预定义的标记基因集被发现并应用于各种基因组研究，然而这些基因集可能不适合新的、未培养的、草稿的或不完整的基因组。因此，在一组具有不同组装质量的基因组中自动识别标记基因集已成为推断微生物种群可靠的系统发育关系的重要任务。开发了一种计算流水线ezTree，用于自动识别一组基因组的单拷贝标记基因，并根据标记基因构建系统发育树。EzTree在一组变形杆菌上的测试表明，ezTree在定位标记基因和构建不同细菌基因组组的可靠树方面非常有效。将ezTree应用于最近从元基因组中回收的基因组，也表明ezTree可以帮助阐明新回收的基因组和现有基因组之间的分类关系。EzTree的开发可以帮助科学家为从环境样本中提取的未耕种物种建立可靠的系统发育树。已发现的单拷贝标记基因也可能为理解一组微生物的共同特征提供关键线索。在GNU GPLv3许可下，ezTree管道可以在https://github.com/yuwwu/ezTree上免费获得。本文的在线版本(10.1186/s12864-0174327-9)包含补充材料，可供授权用户使用。
Inferring phylogenetic trees for newly recovered genomes from metagenomic samples is very useful in determining the identities of uncultivated microorganisms. Even though 16S ribosomal RNA small subunit genes have been established as “gold standard” markers for inferring phylogenetic trees, they usually cannot be assembled very well in metagenomes due to shared regions among 16S genes. Using single-copy marker genes to build genome trees has become increasingly popular for uncultivated species. Predefined marker gene sets were discovered and have been applied in various genomic studies; however these gene sets might not be adequate for novel, uncultivated, draft, or incomplete genomes. The automatic identification of marker gene sets among a set of genomes with different assembly qualities has thus become a very important task for inferring reliable phylogenetic relationships for microbial populations. A computational pipeline, ezTree, was developed to automatically identify single-copy marker genes for a group of genomes and build phylogenetic trees from the marker genes. Testing ezTree on a group of proteobacteria species revealed that ezTree was highly effective in pinpointing marker genes and constructing reliable trees for different groups of bacterial genomes. Applying ezTree to genomes that were recently recovered from metagenomes also showed that ezTree can help elucidate taxonomic relationships among newly recovered genomes and existing ones. The development of ezTree can help scientists build reliable phylogenetic trees for uncultivated species retrieved from environmental samples. The uncovered single-copy marker genes may also provide crucial hints for understanding shared features of a group of microbes. The ezTree pipeline is freely available at https://github.com/yuwwu/ezTree under a GNU GPLv3 license. The online version of this article (10.1186/s12864-017-4327-9) contains supplementary material, which is available to authorized users.
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