Santos Liliana, Alves Artur, Alves Rui
Departamento de Biologia, CESAM, Universidade de Aveiro , Aveiro , Portugal.
Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida and IRBLleida , Lleida , Spain.
PeerJ. 2017 Mar 28;5:e3120. doi: 10.7717/peerj.3120. eCollection 2017.
Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus . Accurate species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.
Here we addressed that problem by identifying five loci that have been sequenced in 142 isolates representing 96 species: , , , and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.
As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the --- 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.
Our results question the current use of the ITS locus for DNA barcoding in the genus and suggest that might be a better choice if one locus barcoding needs to be done.
物种鉴定对于控制病害、理解流行病学以及指导针对该属真菌实施植物检疫措施至关重要。准确的物种区分需要使用多位点系统发育树。然而，确定可用于物种鉴定的最佳位点组合仍是一个未解决的问题。
在此，我们通过鉴定在代表96个物种的142个分离株中已测序的五个位点来解决该问题： 、 、 、 和ITS。然后，我们使用这些位点的每一种可能组合来构建、分析和比较系统发育树。
正如预期的那样，当同时使用所有五个位点来构建分离株的系统发育树时，物种区分效果更好。然而，去除ITS位点对重建的系统发育树影响不大，这表明 --- 4位点树几乎等同于5位点树。我们进一步确定了该属中用于物种区分的最佳3位点、2位点和1位点树。
我们的结果对目前在该属中使用ITS位点进行DNA条形码分析提出了质疑，并表明如果需要进行单一位点条形码分析， 可能是更好的选择。
