Abstract
Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark—the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.
Highlights
The basidiomycetous yeast Phaffia rhodozyma, formerly known as Xanthophyllomyces dendrorhous [1,2], is the only fungus known to produce astaxanthin [3], an economically relevant carotenoid [4]
Representatives of six genera of the Cystofilobasidiales were included in the phylogeny depicted in Figure 1 that confirmed that Cystofilobasidium and Phaffia are sister genera
Our previous results obtained using both housekeeping genes and genes encoding enzymes of the astaxanthin biosynthetic pathway support the recognition of two new Phaffia species, as the divergence between the proposed three species clearly exceeds the documented divergence between the various populations of P. rhodozyma [13]
Summary
The basidiomycetous yeast Phaffia rhodozyma, formerly known as Xanthophyllomyces dendrorhous [1,2], is the only fungus known to produce astaxanthin [3], an economically relevant carotenoid [4]. The majority of the commercially available astaxanthin is produced by chemical synthesis, environmental and food safety concerns are driving the development of economically viable natural sources of this carotenoid, involving genetic engineering of P. rhodozyma among other approaches [7,8,9]. Six genes are known to be involved in the synthesis of astaxanthin in P. rhodozyma, which starts in the mevalonate pathway that forms isopentenylpyrophosphate (IPP), the general precursor of all isoprenoids [10]. The production of β-carotene in P. rhodozyma occurs in a similar way to other carotenogenic fungi, it is the final step performed by CrtS that sets P. rhodozyma apart and allows for its unique ability to produce astaxanthin [11]
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