Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis
Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis
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DOI：
10.1111/1758-2229.12455
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发表时间：
2016-10-01
影响因子：
3.3
通讯作者：
Zehr, Jonathan P.
中科院分区：
文献类型：
--
作者：
Frank, Ildiko E.;Turk-Kubo, Kendra A.;Zehr, Jonathan P.
nifH基因是研究固氮作用的一个广泛使用的分子代理。nifH基因序列的系统发育分类是重氮养菌群落分析的重要步骤，由于环境序列文库的规模不断增加，高通量技术提高了nifH序列的产量，因此需要快速的自动化解决方案。提出了一种新的方法来快速分类nifH氨基酸序列进入定义良好的系统发育集群，为跨研究的比较分析提供了一个共同的平台。系统发育类群归属可以通过决策树型统计模型准确预测，该模型可以识别和利用氨基酸序列中的特征残基。我们的分类模型是通过包含聚类注释的公开可用的人工管理的nifH基因数据库进行训练和评估的。利用来自不同生态系统的独立于模型的序列集进一步评估模型的预测精度。在一项比较研究中证明了这种新的序列分类方法的实用性，该研究对来自广泛栖息地的重氮营养菌组合进行联合处理，确定了栖息地特异性和广泛分布的重氮营养菌，并揭示了群落组成的海洋-陆地差异。我们快速和自动化的系统发育聚类分配避免了对nifH序列进行广泛的系统发育分析；因此，为固氮研究节省了大量的时间和资源。
The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.