Ribosomal RNA of Metchnikovellids in Gregarine Transcriptomes and rDNA of Microsporidia Sensu Lato in Metagenomes

— Numerous nucleotide sequences of microsporidia sensu lato , mainly belonging to the “Cryptomycota” (Rozellida, Rozellomycota, Rozellosporidia, treated here as synonyms), are found in metagenomes, transcriptomes, and amplicon libraries used for metabarcoding. In this study, we describe rDNA sequences of hyperparasitic metchnikovellid microsporidia found in the transcriptomes of unicellular protists belonging to Apicomplexa (Alveolata). The transcriptome of the eugregarine Polyrhabdina sp. (GenBank SRX6640468) contains the cDNA of Metchnikovella incurvata , the transcriptome of the archigregarine Selenidium pygospionis (GenBank SRX6640459) contains the cDNA of Metchnikovella dogieli , and in the transcriptome of the blastogregarine Siedleckia cf. nematoides (GenBank SRX6640464) we find cDNAs originating from a yet undescribed species representing a novel metchnikovellid family. We have modeled the secondary structure of the “ITS2” region of identified and unidentified metchnikovellids taking into account the covariant nucleotide substitutions. Based on the predicted secondary structure of rRNA, mapping of reads from cDNA libraries, and the absence of the endoribonuclease Las1 (PF04031), we conclude that there is no ITS2 processing in metchnikovellids, and the mature “5.8S”- and “28S”-like (LSU) rRNA are covalently fused, similarly to the LSU rRNA in the other microsporidia sensu stricto . We discuss several previously proposed ( Chytridiopsis typographi , BAQA065) and new candidates for the sister group of microsporidia sensu stricto , and compare the reduced rRNA genes of microsporidia and the lengthened rRNA genes with group I introns of parasitic and lichen fungi in the context of neutral and adaptive evolutionary processes.