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

Publication ,  Journal Article
Bellora, N; Moliné, M; David-Palma, M; Coelho, MA; Hittinger, CT; Sampaio, JP; Gonçalves, P; Libkind, D
Published in: BMC genomics
November 2016

The class Tremellomycete (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 of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed.Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the 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 potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated.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.

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Published In

BMC genomics

DOI

EISSN

1471-2164

ISSN

1471-2164

Publication Date

November 2016

Volume

17

Issue

1

Start / End Page

901

Related Subject Headings

  • Ultraviolet Rays
  • Reproduction, Asexual
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Genome, Fungal
  • Genetic Variation
  • Gene Order
  • Computational Biology
  • Catalase
  • Bioinformatics
 

Citation

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Bellora, N., Moliné, M., David-Palma, M., Coelho, M. A., Hittinger, C. T., Sampaio, J. P., … Libkind, D. (2016). Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC Genomics, 17(1), 901. https://doi.org/10.1186/s12864-016-3244-7
Bellora, Nicolás, Martín Moliné, Márcia David-Palma, Marco A. Coelho, Chris Todd Hittinger, José P. Sampaio, Paula Gonçalves, and Diego Libkind. “Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.BMC Genomics 17, no. 1 (November 2016): 901. https://doi.org/10.1186/s12864-016-3244-7.
Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, Sampaio JP, et al. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC genomics. 2016 Nov;17(1):901.
Bellora, Nicolás, et al. “Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.BMC Genomics, vol. 17, no. 1, Nov. 2016, p. 901. Epmc, doi:10.1186/s12864-016-3244-7.
Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, Sampaio JP, Gonçalves P, Libkind D. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC genomics. 2016 Nov;17(1):901.
Journal cover image

Published In

BMC genomics

DOI

EISSN

1471-2164

ISSN

1471-2164

Publication Date

November 2016

Volume

17

Issue

1

Start / End Page

901

Related Subject Headings

  • Ultraviolet Rays
  • Reproduction, Asexual
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Genome, Fungal
  • Genetic Variation
  • Gene Order
  • Computational Biology
  • Catalase
  • Bioinformatics