Why it’s important
Fungal genomes are rarely well characterized in public databases. Other than highly relevant model organisms like Saccharomyces cerevisiae, most available fungal genomes are highly fragmented, which presents difficulties for further genomic analyses. In the case of H. roseonigra (ATCC 20624), no member of the Hyphozyma genus has ever had its full genome sequence published. Due to the lack of public data on Hyphozyma, research on H. roseonigra is particularly limited, which is detrimental as it is the only reported strain capable of degrading sclareol to sclareol glycol.1
Sclareol glycol is a precursor of ambroxide, which is a key substitute for ambergris. Ambergris is a highly valuable and increasingly scarce fixative that prolongs the longevity of the aroma in a perfume. This fixative, however, is produced in the digestive system of certain whales and is no longer legal to trade in many countries. In an effort to protect endangered whales, there has been a shift in the fragrance industry to rely on ambroxide, a more environmentally conscious substitute.
Currently, Cryptococcus albidus is often used in the process to create ambroxide, though it cannot directly produce the precursor for ambroxide.2 Other synthetic methods to produce ambroxide or (-)-ambrox involve the use of specific plants that produce diterpenoids, though these are only created in small mixtures of other natural products.3 In contrast, H. roseonigra, shows great promise in that it can condense the production process and directly generate the precursor molecule under more laboratory-friendly conditions.
What’s the solution?
With the publication of the H. roseonigra (ATCC 20624) full genome sequence to the ATCC Genome Portal, the first step has been made to better understand members of the Hyphozyma genus and to renewing research into H. roseonigra and its prospective role in the fragrance industry.
How we can help
As part of our initiative to enhance the authentication of our microbial products, ATCC will continue to sequence and assemble genomes of organisms from our repository, paying special attention to those that have never been previously published on public databases. If you know of any such organisms that you would like for ATCC to focus our efforts into publishing on the ATCC Genome Portal send them to us.
Biological data experts
Nikhita Puthuveetil, MS
Senior Bioinformatician, Sequencing and Bioinformatics Center, ATCC
Nikhita Puthuveetil is a bioinformatician at ATCC that performs routine bioinformatics analysis on internal sequencing submissions, primarily SARS-CoV-2 samples as well as plasmid and bacterial samples. She also works with her team to aid in the development of the ATCC Genome Portal. She first joined ATCC as an bioinformatics intern in 2019 where she worked to create an internal sequencing dashboard in R to track and manage sequencing at the Sequencing and Bioinformatics Center. She has an MS in Bioinformatics from Virginia Commonwealth University.
David Yarmosh, MS
Lead Bioinformatician, ATCC
David Yarmosh is a lead bioinformatician in ATCC’s Sequencing and Bioinformatics Center. He’s a graduate of New York University’s Tandon School of Engineering. He has been working in large data aggregation and analysis since 2013 and microbial genomics with a focus on biosurveillance R&D efforts since 2016. David has led international training exercises in Peru and Senegal, sharing metagenomic analytical capabilities. His interests include genomics database construction, metadata collection, drug resistance mechanisms, bioinformatics standards, and machine learning. Since joining ATCC in 2020, David has worked extensively in SARS-CoV-2 classification, epidemiology, and genomics evaluation, including enhanced and uniform variant reporting. He has contributed more broadly to genomics reporting and analytical standardization and he has helped develop the podcast Behind the Biology, which he now hosts.
Sung-Oui Suh, PhD
Scientist, ATCC
Sung-Oui Suh, Ph.D., is a scientist at ATCC. He has over 25 years of training in the fields of mycology and molecular ecology, with extensive experience in studies on microorganisms in various environments, such as those associated with insects, plants, humans, and animals. His current research focuses on developing rapid identification tools for medically and industrially relevant yeasts and fungi.
Authentication and sequencing tools
Discover the ATCC Genome Portal
The ATCC Genome Portal is a rapidly growing ISO 9001–compliant database of high-quality reference genomes from authenticated microbial strains in the ATCC collection. Through this cloud-based platform, you can easily access and download meticulously curated whole-genome sequences from your browser or our secure API. With high-quality, annotated data at your fingertips, you can confidently perform bioinformatics analyses and make insightful correlations.
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Podcast
Episode 1: The Difficulties of Big Data in the Biological Sciences
Learn about issues such as reproducibility in research, the pros and cons of crowd sourcing data, and a solution in ATCC’s approach to whole-genome sequencing, assembly, and annotation for producing high-quality, authenticated reference genomes
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References
1. Farbood MI, Willis BJ (1986) Process for producing diol and furan and microorganism capable of same. US Patent 4,798,799.
2. Wang X, Zhang X, Yao Q, Hua D, Qin J. Comparative proteomic analyses of Hyphozyma roseonigra ATCC 20624 in response to sclareol. Braz J Microbiol. 2019 Jan;50(1):79-84. doi: 10.1007/s42770-019-00040-2. Epub 2019 Jan 15. PMID: 30645731; PMCID: PMC6863283.
3. Zerbe P, Bohlmann J. Enzymes for synthetic biology of ambroxide-related diterpenoid fragrance compounds. Adv Biochem Eng Biotechnol. 2015;148:427-47. doi: 10.1007/10_2015_308. PMID: 25846965.
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