TreeOTU

Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms, especially the bacteria and archaea, is mostly based upon studies of sequences of the small- subunit rRNAs (ssu-rRNAs). To address the limitation of ssu-rRNA as a phylogenetic marker, such as copy number variation among organisms and complications introduced by horizontal gene transfer, convergent evolution, or evolution rate variations, we have identified protein- coding gene families as alternative Phylogenetic and Phylogenetic Ecology markers (PhyEco). Current nucleotide sequence similarity based Operational Taxonomic Unit (OTU) classification methods are not readily applicable to amino acid sequences of PhyEco markers. We report here the development of TreeOTU, a phylogenetic tree structure based OTU classification method that takes into account of differences in rates of evolution between taxa and between genes. OTU sets built by TreeOTU are more faithful to phylogenetic tree structures than sequence clustering (non phylogenetic) methods for ssu-rRNAs. OTUs built from phylogenetic trees of protein coding PhyEco markers are comparable to our current taxonomic classification at different levels. With the included OTU comparing tools, the TreeOTU is robust in phylogenetic referencing with different phylogenetic markers and trees. The TreeOTU package includes OTU classification, comparison and tree rooting scripts, as well as the alignments, trees and NCBI/IMG taxonomic classification information related to this research. The contents in he package are described in the file README.txt.目前我们对细胞生物（尤其是细菌与古菌）的分类学与系统发育多样性的认知，大多基于对小亚基核糖体RNA（small-subunit rRNA, ssu-rRNA）序列的研究。为解决ssu-rRNA作为系统发育标记物的局限性——例如不同生物间的拷贝数变异，以及水平基因转移、趋同演化或进化速率差异带来的分析复杂性——我们将蛋白质编码基因家族确定为替代性的系统发育与系统发育生态标记物（Phylogenetic and Phylogenetic Ecology markers, PhyEco）。当前基于核苷酸序列相似性的操作分类单元（Operational Taxonomic Unit, OTU）分类方法，难以直接适用于PhyEco标记物的氨基酸序列。本研究报道了TreeOTU的开发：这是一种基于系统发育树结构的OTU分类方法，可兼顾不同类群与不同基因间的进化速率差异。相较于针对ssu-rRNA的序列聚类（非系统发育类）方法，TreeOTU生成的OTU集合与系统发育树结构的契合度更高。基于蛋白质编码型PhyEco标记物系统发育树构建的OTU，可与不同层级的现行分类学分类结果相匹配。借助内置的OTU比对工具，TreeOTU在使用不同系统发育标记物与系统发育树开展系统发育参照分析时具备较强的稳健性。TreeOTU工具包包含OTU分类、比对以及系统发育树根化脚本，同时涵盖本研究相关的序列比对（alignment）结果、系统发育树以及NCBI/IMG分类学分类信息。该工具包的具体内容详见README.txt文件。