Intragenomic variation is the molecular variation within the genome among repetitive DNA. As a multigene family, nuclear ribosomal DNA (rDNA) has been widely used in fungal taxonomy for their ease in amplification and suitable variability to attain various levels of taxonomic resolution. At the intraspecific level, rDNA is believed to be under concerted evolution and the internal transcribed spacers (ITS) region is actually accepted as a universal barcoding marker for fungi. However, documentation of intragenomic variation of rDNA indicated that it can be problematic in species delimitation and identification. Fungal taxonomic studies have not generally taken into account the intragenomic variation of rDNA in a systematic manner. In this review, our objective is to address the definition, the origin and the mechanisms for maintenance of intragenomic variation, as well as its implication in the domain of fungal molecular taxonomy, particularly for species delimitation, identification and DNA barcoding. With advanced sequencing technologies (second and third generations), we also addressed how these technologies can be used to study the intragenomic variation of rDNA and also how the intragenomic variation will impact on DNA barcoding via high-throughput sequencing.

基因组内变异是基因组内重复 DNA 之间的分子变异。作为一个多基因家族，核糖体 DNA (rDNA) 因其易于扩增和适当的变异性而被广泛用于真菌分类学，以达到不同水平的分类学分辨率。在种内水平，rDNA 被认为是协同进化，内部转录间隔 (ITS) 区域实际上被接受为真菌的通用条形码标记。然而，rDNA 基因组内变异的文件表明它在物种定界和鉴定中可能存在问题。真菌分类学研究通常没有系统地考虑 rDNA 的基因组内变异。在这次审查中，我们的目标是解决定义，基因组内变异的起源和维持机制，以及它在真菌分子分类学领域的意义，特别是在物种定界、鉴定和 DNA 条形码方面。借助先进的测序技术（第二代和第三代），我们还讨论了如何使用这些技术来研究 rDNA 的基因组内变异，以及基因组内变异将如何通过高通量测序影响 DNA 条形码。