van Ingen-Buijs Valerie A, van Westerhoven Anouk C, Skiadas Petros, Zuijdgeest Xander C L, Haridas Sajeet, Daum Christopher, Duffy Kecia, Guo Jie, Hundley Hope, LaButti Kurt, Lipzen Anna, Pangilinan Jasmyn, Riley Robert, Wang Jie, Yan Mi, Martin Francis, Barry Kerrie, Grigoriev Igor V, Groenewald Johannes Z, Crous Pedro W, Seidl Michael F
Evolutionary Phytopathology group, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, the Netherlands; Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, the Netherlands; Netherlands Institute for Vectors, Invasive plants and Plant Health (NIVIP), National Plant Protection Organization (NPPO), Netherlands Food and Consumer Product Safety Authority (NVWA), Geertjesweg 15, 6706 EA, Wageningen, the Netherlands.
Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, the Netherlands; Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, the Netherlands.
Fungal Genet Biol. 2024 Dec;175:103925. doi: 10.1016/j.fgb.2024.103925. Epub 2024 Sep 5.
Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.
柑橘叶点霉是一种重要的柑橘病原菌，在欧盟属于检疫性生物。其最近被描述的近缘种——副柑橘叶点霉，与之关系非常密切，且未被列为检疫性生物。副柑橘叶点霉很难与柑橘叶点霉区分开来，因为它们的形态特征相互重叠，而且最初用于将它们界定为不同物种的条形码基因序列中，物种特异性多态性数量较少，随后发现这两个进化枝之间的这些序列也有重叠。因此，我们进行了广泛的基因组分析，以确定柑橘叶点霉和副柑橘叶点霉菌株之间的遗传变异应被视为柑橘叶点霉种内变异，还是表明它们是不同的物种。通过使用包含3000个单拷贝直系同源基因的系统基因组分析和全基因组比较，我们确定柑橘叶点霉和副柑橘叶点霉之间的变异可被视为柑橘叶点霉种内变异。我们还确定了几种叶点霉菌种线粒体组装体的变异水平，并得出结论：柑橘叶点霉和副柑橘叶点霉的组装体之间只有极小的差异。因此，通过几种正交方法，我们在此证明，其他叶点霉菌种的核基因组和线粒体基因组内的变异大于从柑橘叶点霉和副柑橘叶点霉菌株获得的基因组之间的变异。因此，柑橘叶点霉和副柑橘叶点霉应被视为同种。
