Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi.
Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi.
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DOI：
10.1371/journal.pone.0018803
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发表时间：
2011-04-13
期刊：
影响因子：
3.7
通讯作者：
Dutech C
中科院分区：
文献类型：
--
作者：
Feau N;Decourcelle T;Husson C;Desprez-Loustau ML;Dutech C
从历史上看，真菌多基因的系统发育是基于少数常用基因的可用性而重建的。这些资源的交叉利用是研究绝大多数非模型真菌（即“孤儿”）的系统发育关系解决了这个问题，我们开发了一种方法，加上一个名为“ Teylorph”的程序（孤儿的系统发育标记）。在低分类水平（例如，在物种复合物中），非模型真菌物种，以最大程度地靶向具有信息区域的基因基于核差异相对于替代类型的估计来显示图形评估系统。 15最佳的候选基因由Thyorph提出的测序成功。真菌系统发育（例如核RDNA，β-微管蛋白，γ-肌动蛋白，伸长因子EF-1α）排名最佳，并在四个非模型的真菌组中的每个非模型中都准确地分类。我们设想，系统将构成一个有用的工具，用于获得新的和准确的系统发育标记，以解决密切相关的非模型真菌物种之间的关系。
Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species.
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