Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

NICOLAS BELLORA; MARTÍN MOLINÉ; MARCIA DAVID-PALMA; MARCO A. COELHO; CHRIS HITTINGER; JOSÉ PAULO SAMPAIO; PAULA GONCALVES; DIEGO LIBKIND

BMC GENOMICS

BIOMED CENTRAL LTD

Lugar: Londres; Año: 2016 vol. 17 p. 901 - 917

1471-2164

Background: The tremellomycete class (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim was to obtain, analyze, and compare two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in mating were analyzed.Results: Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Comparison of their genomes with other fungi revealed that P. rhodozyma strains (and other Cystofilobasidiales) have the highest number of intron-containing genes and highest number of introns per gene among fungi. The Patagonian strain showed 4.4% of nucleotide sequence divergence compared to both European strains (which differed from each other by only 0.073%). All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster that is potentially responsible for photoprotection (mycosporines) was found in our P. rhodozyma strains but was not present in CBS 6938 (non-mycosporinogenic). A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, most genes related to meiosis were found and annotated. Conclusions: A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome.