## 1 Introduction  
The nosemosis type C is a disease of honey bees caused by the macroscoparium _Nosema ceranae_[1, 2]. The parasite, native of the Asian honey bee _Apis cerana_[3], spread rapidly around the world becoming one of the diseases causing colony decline and collapse in the European honey bee _Apis mellifera_, often replacing _Nosema apis_[4, 5, 6, 7, 8]. The microsporidium is an intracellular obligate parasite with high tropism for the honey bee ventriculium [3, 9, 10], infecting its epithelial cells to replicate [11]. Usually, the _N. ceranae_ infection tends to be asymptomatic, but in symptomatic individuals [5, 12], the disease may be shortening the lifespan of workers, inducing lethargic behavior and reducing the foraging activity [9, 13, 14]. _N. ceranae_ represents an important threat for pollinators and hypmenopterans, other than honey bees [15, 16, 17, 18, 19, 20, 21]. Although the transmission routes remain unknown [15, 22], _N. ceranae_ spores were found in the hive pest _Aethina tumida_ and the regurgitated pellets of the bee-eater _Merops apiaster_[23, 24]  
All microsporidia have very small genomes, usually less than 20 million megabases (Mb) [25]. The _N. ceranae_ genome appears to be approximately 7.86 Mb [26], similarly to _N. apis_ (8.50 Mb) [27]. The ribosomal DNA (rDNA) represents the portion of DNA coding for the RNA that makes up the ribosomes of a living organism (rRNA) [28]. Typically, rDNA is organized within the genome in repeated copies in tandem. Each copy represents a well-defined unit, which is made up of two main components: Small Sub Unit rDNA (SSU-rDNA) and Large Sub Unit rDNA (LSU-rDNA), which represent the coding sequences for the rRNAs that will, respectively, constitute the minor and major subunits of the ribosome [29]. The rRNAs, depending on their sedimentation coefficient, take on different names in various living organisms. In the case of _N. ceranae_ the SSU-rRNA is represented as _16S_, while the LSU-rRNA as _18S_. The two coding sequences are separated from each other by a non-coding one called Internal Transcribed Spacer (ITS), while between each repeated unit of rDNA there is another non-coding sequence called Intergenic Spacer (IGS) [29]. These DNA sequences are frequently used for phylogenetic studies of eukaryotic organisms [1], and the same approach was used to study _N. ceranae_ also [3]. Therefore, rDNA has also been used to distinguish the different species belonging to the genus _Nosema_, especially _N. ceranae_ from _N. apis_, both capable of infecting _A. mellifera_[30; 31; 32; 33], as well as to evaluate the degree of intraspecific variability of those two microsporidia [31; 34; 35].In general, the quantification of _N. ceranae_ abundance relies on primer pairs designed on different sequences of the same SSU-rRNA (_16S rRNA_) [36]. The first contribution of _N. ceranae_ genome highlighted the possible presence of multiple copies of rDNA [26]. Various subsequent studies demonstrated their existence, and revealed a high degree of polymorphism between them [6; 34; 37]. Additionally, in other microsporidia, e.g. _Encephalizoon cuniculi_, multiple copies of ribosomal genes are present, albeit they are homogeneous within the same genome [38]. The point that ribosomal genes are repeated within the genome is considered normal in eukaryotes. However, the repetitions are usually homogeneous or denote minimal variations in their sequences [39]. That occurs thanks to the phenomenon of concerted evolution, normally defined as the process by which the paralogous genes (genes repeated within the genome) present in a given species show greater sequence similarity compared to ortholog genes (genes with different origins but with similar functions) present in other related species [40]. Concerted evolution, therefore, provides for molecular mechanisms that prevent the independent evolution of repeated sequences, keeping them homogeneous within the genome. Ribosomal genes are among the best known examples of concerted evolution [39].