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Background   Blastocladiella emersonii  is an aquatic fungus of the Chytridiomycete class, which is at the base of the fungal phylogenetic tree. In this sense, some ancestral characteristics of fungi and animals or fungi and plants could have been retained in this aquatic fungus and lost in members of late-diverging fungal species. To identify in  B. emersonii  sequences associated with these ancestral characteristics two approaches were followed: (1) a large-scale comparative analysis between putative unigene sequences ( uniseqs ) from  B. emersonii  and three databases constructed  ad hoc  with fungal proteins, animal proteins and plant unigenes deposited in Genbank, and (2) a pairwise comparison between  B. emersonii  full-length cDNA sequences and their putative orthologues in the ascomycete  Neurospora crassa  and the basidiomycete  Ustilago maydis .    Results  Comparative analyses of  B. emersonii uniseqs  with fungi, animal and plant databases through the two approaches mentioned above produced 166  B. emersonii  sequences, which were identified as putatively absent from other fungi or not previously described. Through these approaches we found: (1) possible orthologues of genes previously identified as specific to animals and/or plants, and (2) genes conserved in fungi, but with a large difference in divergence rate in  B. emersonii . Among these sequences, we observed cDNAs encoding enzymes from coenzyme B 12 -dependent propionyl-CoA pathway, a metabolic route not previously described in fungi, and validated their expression in Northern blots.    Conclusion  Using two different approaches involving comparative sequence analyses, we could identify sequences from the early-diverging fungus  B. emersonii  previously considered specific to animals or plants, and highly divergent sequences from the same fungus relative to other fungi.

Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii