The internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA) has been established (and is generally accepted) as a primary “universal” genetic barcode for fungi for many years, but the actual value for taxonomy has been heavily disputed among mycologists. Recently, twelve draft genome sequences, mainly derived from type species of the family Hypoxylaceae (Xylariales, Ascomycota) and the ex-epitype strain of Xylaria hypoxylon have become available during the course of a large phylogenomic study that was primarily aimed at establishing a correlation between the existing multi-gene-based genealogy with a genome-based phylogeny and the discovery of novel biosynthetic gene clusters encoding for secondary metabolites. The genome sequences were obtained using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing, respectively, and resulted in high-quality sequences with an average N50 of 3.2 Mbp. While the main results will be published concurrently in a separate paper, the current case study was dedicated to the detection of ITS nrDNA copies in the genomes, in an attempt to explain certain incongruities and apparent mismatches between phenotypes and genotypes that had been observed during previous polyphasic studies. The results revealed that all of the studied strains had at least three copies of rDNA in their genomes, with Hypoxylon fragiforme having at least 19 copies of the ITS region, followed by Xylaria hypoxylon with at least 13 copies. Several of the genomes contained 2–3 copies that were nearly identical, but in some cases drastic differences, below 97% identity were observed. In one case, ascribable to the presence of a pseudogene, the deviations of the ITS sequences from the same genome resulted in only ca. 90% of overall homology. These results are discussed in the scope of the current trends to use ITS data for species recognition and segregation of fungi. We propose that additional genomes should be checked for such ITS polymorphisms to reassess the validity of this non-coding part of the fungal DNA for molecular identification.

中文翻译：

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猪舌科（Xylariales，Ascomycota）高质量基因组ITS区的Intragenomic多态性

核糖体DNA（rDNA）的内部转录间隔区（ITS）区已经被确立（并被普遍接受）作为真菌的主要“通用”遗传条形码，但是分类学的实际价值在真菌学家中引起了很大争议。 。最近，有十二个基因组草图序列，主要来自猪舌亚科（Xylariales，Ascomycota）的类型物种和Xyaria hypoxylon的前表型菌株。在大型系统生物学研究的过程中，已经获得了有效的信息，该研究的主要目的是建立现有的基于多基因的家谱与基于基因组的系统发育之间的关联，以及发现编码次级代谢产物的新型生物合成基因簇之间的相关性。分别使用Illumina和Oxford纳米孔技术或PacBio测序获得了基因组序列，并产生了平均N50为3.2 Mbp的高质量序列。虽然主要结果将同时发表在另一篇论文上，但当前的案例研究致力于检测基因组中的ITS nrDNA拷贝，以试图解释在先前的研究中已观察到的表型与基因型之间的某些不一致和明显错配多相研究。炭团fragiforme具有ITS区域的至少19份，接着炭角炭团与至少13份。几个基因组包含2-3个几乎相同的拷贝，但是在某些情况下，差异很大，观察到的一致性低于97％。在一种情况下，归因于假基因的存在，ITS序列与同一基因组的偏离仅导致大约1。总体同源性的90％。这些结果将在当前使用ITS数据进行物种识别和真菌分离的趋势范围内进行讨论。我们建议应检查其他基因组的ITS多态性，以重新评估真菌DNA的这一非编码部分用于分子鉴定的有效性。