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Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane- and cell-wall-associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.

Systematics of Chytridiales has been deeply influenced by analyses of molecular loci and zoospore ultrastructure. Even though the Chytridiales is the largest order within Chytridiomycota, Brazilian isolates of this clade have been poorly integrated. Here, we isolated seven species and documented their morphology, including zoospore ultrastructure for Siphonaria aurea , and phylogenetic positions for all based on analyses of nuc 18S and 28S rDNA. Phylogenetic results support the placement of these species in Chytriomycetaceae and Chytridiaceae, with two new species described, Rhizidium crepaturum and Siphonaria aurea , and Rodmanochytrium sphaericum recorded for the first time from Brazil.

Six Nowakowskiella species from Brazil were identified and purified on corn meal agar (CMA) plus glucose and Peptonized Milk-Tryptone-Glucose (PmTG) media and placed into a phylogenetic framework for the genus. New sequence data are presented for four species: N. elongata, N. multispora , and N. ramosa and the new species N. crenulata . Our maximum likelihood and Bayesian analyses of combined 18S, 5.8S, and 28S subunits of nuc rDNA showed that Nowakowskiella is not a monophyletic clade because of the position of Nowakowskiella elongata , which is more related to Cladochytrium . We reclassify N. elongata as the type of a new genus, Karlingiella .