Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins

We have determined complete gene sequences encoding the largest subunit of the RNA polymerase II (RBP1) from two Microsporidia, Vairimorpha necatrix a nd Nosema locustae. Phylogenetic analyses of these and other RPB1 sequences strongly support the notion that Microsporidia are not early-diverging euk aryotes but instead are specifically related to Fungi. Our reexamination of elongation factors EF-1 alpha and EF-2 sequence data that had previously b een taken as support for an early (Archezoan) divergence of these amitochon driate protists show such support to be weak and likely caused by artifacts in phylogenetic analyses. These EF data sets are, in fact, not inconsisten t with a Microsporidia + Fungi relationship. In addition, we show that none of these proteins strongly support a deep divergence of Parabasalia and Me tamonada, the other amitochondriate protist groups currently thought to com pose early branches. Thus, the phylogenetic placement among eukaryotes for these protist taxa is in need of further critical examination.