Genomic analysis of the astaxanthin producing yeast Phaffia rhodozyma (Xanthophyllomyces dendrorhous) with special focus on antioxidant-related genes

DIEGO LIBKIND; MARTÍN MOLINÉ; NICOLAS BELLORA; CHRIS HITTINGER; MARÍA ROSA GIRAUDO DE VAN BROOCK

Congreso; Comparative Genomics of Eukaryotic Microorganisms: Understanding The Complexity of Diversity; 2011

European Molecular Biology Organization

The basidiomycetous yeast Phaffia rhodozyma (Xanthophyllomyces dendrorhous) produces a battery of biotechnologically relevant compounds including the pigment astaxanthin which is commercially exploited for aquaculture feeds and the UV absorbing compound mycosporine-glutaminol-glucoside (MGG), a potential UV-sunscreen. We obtained a draft version of the complete genome sequence of strains CBS7918T (11x coverage) and CRUB1149 (16x) by short paired-end sequencing (Illumina) and de novo assembly (N50=120Kb). We obtained a 19Mb genome with a 47.3% G+C content. Sequence error rate was below 0.1% and 98% of the 275KB from 150 P. rhodozyma sequences available at NCBI were covered. Preliminary results suggest that Phaffia has a multipartite mitochondrial genome of 20Kb, as seen in other Cystofilobasidiales. Comparative analysis showed an average 3-5% DNA divergence between conspecific strains. 5024 genes were preliminary annotated and a comparative analysis of 1457 protein sequences showed low similarity values (45%) between Phaffia and Cryptococcus neoformans (closest relative with available genome). Genome mining allowed the localization of the astaxanthin synthesizing genes and new putative regulatory enzymes, and as well as the identification of the hitherto unknown gene cluster responsible for MGG synthesis. This cluster contained three genes (DHQS-like, O-Methyl-transferase and ATP-grasp) common to other mycosporine-producing organisms though with significant modifications. When compared to related fungi, limited antioxidant enzymes were found: 2 MnSOD and 3 catalases, suggesting that Phaffia has multiple antioxidant strategies probably due to the environmental stress imposed in its natural habitat. In this paper, the complete genomic sequence of this unique yeast of great biotechnological importance is presented and analyzed.