Abstract
BackgroundMicrosporidia is one of the taxa that have experienced the most dramatic taxonomic reclassifications. Once thought to be among the earliest diverging eukaryotes, the fungal nature of this group of intracellular pathogens is now widely accepted. However, the specific position of microsporidia within the fungal tree of life is still debated. Due to the presence of accelerated evolutionary rates, phylogenetic analyses involving microsporidia are prone to methodological artifacts, such as long-branch attraction, especially when taxon sampling is limited.ResultsHere we exploit the recent availability of six complete microsporidian genomes to re-assess the long-standing question of their phylogenetic position. We show that microsporidians have a similar low level of conservation of gene neighborhood with other groups of fungi when controlling for the confounding effects of recent segmental duplications. A combined analysis of thousands of gene trees supports a topology in which microsporidia is a sister group to all other sequenced fungi. Moreover, this topology received increased support when less informative trees were discarded. This position of microsporidia was also strongly supported based on the combined analysis of 53 concatenated genes, and was robust to filters controlling for rate heterogeneity, compositional bias, long branch attraction and heterotachy.ConclusionsAltogether, our data strongly support a scenario in which microsporidia is the earliest-diverging clade of sequenced fungi.
Highlights
Microsporidia is one of the taxa that have experienced the most dramatic taxonomic reclassifications
Chromosomal neighborhood conservation analysis We first explored similarities in chromosomal gene order between microsporidia and other clades, which has been used to associate microsporidia and zygomycotina [14]. This was mainly based on comparisons among E. cuniculi, Rhizopus oryzae and other fungi
A recent detailed analysis of the MAT locus found that this organization is likely to be either a derived ancestral opisthokont character or the result of convergence [21]. Besides this particular locus, the generally higher number of neighboring pairs found between E. cuniculi and R. oryzae must be considered carefully too, especially when relaxed criteria for synteny and homology are used
Summary
We exploit the recent availability of six complete microsporidian genomes to re-assess the longstanding question of their phylogenetic position. We show that microsporidians have a similar low level of conservation of gene neighborhood with other groups of fungi when controlling for the confounding effects of recent segmental duplications. A combined analysis of thousands of gene trees supports a topology in which microsporidia is a sister group to all other sequenced fungi. This topology received increased support when less informative trees were discarded. This position of microsporidia was strongly supported based on the combined analysis of 53 concatenated genes, and was robust to filters controlling for rate heterogeneity, compositional bias, long branch attraction and heterotachy
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