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New Trends in Yeast Genomics
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New Trends in Yeast Genomics

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (20 June 2022) | Viewed by 22729

Special Issue Editors

Dr. Ricardo Franco-Duarte

E-Mail Website
Guest Editor
CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal
Interests: yeast biodiversity; yeast genomics; biotechnology; bioinformatics; yeast phenometabolomics
Special Issues, Collections and Topics in MDPI journals
Dr. Celia Pais

E-Mail Website
Guest Editor
CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
Interests: microbial diversity; molecular typing; biotechnology; clinical mycology

Special Issue Information

Dear Colleagues,

Research focusing on the genomic analysis of yeasts has increased considerably in the past few years, being pushed by advances in high-throughput sequencing technologies, development of bioinformatic pipelines, and a better understanding of yeast ecology and diversity. In this Special Issue, we plan to gather research articles focusing on both fundamental and applied research that demonstrate the importance of yeast characterization and evolution and their application in biotechnological processes. The intensive research on yeasts now requires a careful translation to overcome the challenges of finding new isolates with improved biotechnological potential.

Dr. Ricardo Franco-Duarte
Dr. Celia Pais
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genomics
  • phenomics
  • bioinformatics
  • evolution
  • yeast diversity
  • biotechnology
  • yeast improvement

Published Papers (7 papers)

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Research

Jump to: Review

18 pages, 3967 KiB  
Article
Multifarious Translational Regulation during Replicative Aging in Yeast
by Tianyu Zhao, Asaka Chida, Yuichi Shichino, Dongwoo Choi, Masaki Mizunuma, Shintaro Iwasaki and Yoshikazu Ohya
J. Fungi 2022, 8(9), 938; https://doi.org/10.3390/jof8090938 - 05 Sep 2022
Viewed by 2428
Abstract
Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosome profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational [...] Read more.
Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosome profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational efficiency, defined as the number of ribosome footprints normalized to transcript abundance, was compared between young and aged cells for each gene. We identified more than 700 genes with changes greater than twofold during replicative aging. Increased translational efficiency was observed in genes involved in DNA repair and chromosome organization. Decreased translational efficiency was observed in genes encoding ribosome components, transposon Ty1 and Ty2 genes, transcription factor HAC1 gene associated with the unfolded protein response, genes involved in cell wall synthesis and assembly, and ammonium permease genes. Our results provide a global view of translational regulation during replicative aging, in which the pathways involved in various cell functions are translationally regulated and cause diverse phenotypic changes. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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16 pages, 11467 KiB  
Article
Whole Genome Sequencing Shows Genetic Diversity, as Well as Clonal Complex and Gene Polymorphisms Associated with Fluconazole Non-Susceptible Isolates of Candida tropicalis
by Caitlin Keighley, Mailie Gall, Sebastiaan J. van Hal, Catriona L. Halliday, Louis Yi Ann Chai, Kean Lee Chew, Chayanika Biswas, Monica A. Slavin, Wieland Meyer, Vitali Sintchenko and Sharon C. A. Chen
J. Fungi 2022, 8(9), 896; https://doi.org/10.3390/jof8090896 - 23 Aug 2022
Cited by 8 | Viewed by 2189
Abstract
Resistance to azoles in Candida tropicalis is increasing and may be mediated by genetic characteristics. Using whole genome sequencing (WGS), we examined the genetic diversity of 82 bloodstream C. tropicalis isolates from two countries and one ATCC strain in a global context. Multilocus [...] Read more.
Resistance to azoles in Candida tropicalis is increasing and may be mediated by genetic characteristics. Using whole genome sequencing (WGS), we examined the genetic diversity of 82 bloodstream C. tropicalis isolates from two countries and one ATCC strain in a global context. Multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogenies were generated. Minimum inhibitory concentrations (MIC) for antifungal agents were determined using Sensititre YeastOne YO10. Eleven (13.2%) isolates were fluconazole-resistant and 17 (20.5%) were classified as fluconazole-non susceptible (FNS). Together with four Canadian isolates, the genomes of 12 fluconazole-resistant (18 FNS) and 69 fluconazole-susceptible strains were examined for gene mutations associated with drug resistance. Fluconazole-resistant isolates contained a mean of 56 non-synonymous SNPs per isolate in contrast to 36 SNPs in fluconazole-susceptible isolates (interquartile range [IQR] 46–59 vs. 31–48 respectively; p < 0.001). Ten of 18 FNS isolates contained missense ERG11 mutations (amino acid substitutions S154F, Y132F, Y257H). Two echinocandin-non susceptible isolates had homozygous FKS1 mutations (S30P). MLST identified high genetic diversity with 61 diploid sequence types (DSTs), including 53 new DSTs. All four isolates in DST 773 were fluconazole-resistant within clonal complex 2. WGS showed high genetic variation in invasive C. tropicalis; azole resistance was distributed across different lineages but with DST 773 associated with in vitro fluconazole resistance. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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19 pages, 1436 KiB  
Article
Torulaspora delbrueckii Phenotypic and Metabolic Profiling towards Its Biotechnological Exploitation
by Flávia Silva-Sousa, Ticiana Fernandes, Fábio Pereira, Diana Rodrigues, Teresa Rito, Carole Camarasa, Ricardo Franco-Duarte and Maria João Sousa
J. Fungi 2022, 8(6), 569; https://doi.org/10.3390/jof8060569 - 26 May 2022
Cited by 9 | Viewed by 2141
Abstract
Wine is a particularly complex beverage resulting from the combination of several factors, with yeasts being highlighted due to their fundamental role in its development. For many years, non-Saccharomyces yeasts were believed to be sources of spoilage and contamination, but this idea [...] Read more.
Wine is a particularly complex beverage resulting from the combination of several factors, with yeasts being highlighted due to their fundamental role in its development. For many years, non-Saccharomyces yeasts were believed to be sources of spoilage and contamination, but this idea was challenged, and many of these yeasts are starting to be explored for their beneficial input to wine character. Among this group, Torulaspora delbrueckii is gaining relevance within the wine industry, owing to its low volatile acidity production, increased release of aromatic compounds and enhanced color intensity. In addition, this yeast was also attracting interest in other biotechnological areas, such as bread and beer fermentation. In this work, a set of 40 T. delbrueckii strains, of varied geographical and technological origins, was gathered in order to characterize the phenotypic behavior of this species, focusing on different parameters of biotechnological interest. The fermentative performance of the strains was also evaluated through individual fermentations in synthetic grape must with the isolates’ metabolic profile being assessed by HPLC. Data analysis revealed that T. delbrueckii growth is significantly affected by high temperature (37 °C) and ethanol concentrations (up to 18%), alongside 1.5 mM SO2, showing variable fermentative power and yields. Our computation models suggest that the technological origin of the strains seems to prevail over the geographical origin as regards the influence on yeast properties. The inter-strain variability and profile of the products through the fermentative processes reinforce the potential of T. delbrueckii from a biotechnological point of view. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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22 pages, 3359 KiB  
Article
Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626
by Margarida Palma, Stephen Mondo, Mariana Pereira, Érica Vieira, Igor V. Grigoriev and Isabel Sá-Correia
J. Fungi 2022, 8(3), 254; https://doi.org/10.3390/jof8030254 - 01 Mar 2022
Cited by 1 | Viewed by 3275
Abstract
The ascomycetous yeast Candida membranifaciens has been isolated from diverse habitats, including humans, insects, and environmental sources, exhibiting a remarkable ability to use different carbon sources that include pentoses, melibiose, and inulin. In this study, we isolated four C. membranifaciens strains from soil [...] Read more.
The ascomycetous yeast Candida membranifaciens has been isolated from diverse habitats, including humans, insects, and environmental sources, exhibiting a remarkable ability to use different carbon sources that include pentoses, melibiose, and inulin. In this study, we isolated four C. membranifaciens strains from soil and investigated their potential to overproduce riboflavin. C. membranifaciens IST 626 was found to produce the highest concentrations of riboflavin. The volumetric production of this vitamin was higher when C. membranifaciens IST 626 cells were cultured in a commercial medium without iron and when xylose was the available carbon source compared to the same basal medium with glucose. Supplementation of the growth medium with 2 g/L glycine favored the metabolization of xylose, leading to biomass increase and consequent enhancement of riboflavin volumetric production that reached 120 mg/L after 216 h of cultivation. To gain new insights into the molecular basis of riboflavin production and carbon source utilization in this species, the first annotated genome sequence of C. membranifaciens is reported in this article, as well as the result of a comparative genomic analysis with other relevant yeast species. A total of 5619 genes were predicted to be present in C. membranifaciens IST 626 genome sequence (11.5 Mbp). Among them are genes involved in riboflavin biosynthesis, iron homeostasis, and sugar uptake and metabolism. This work put forward C. membranifaciens IST 626 as a riboflavin overproducer and provides valuable molecular data for future development of superior producing strains capable of using the wide range of carbon sources, which is a characteristic trait of the species. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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23 pages, 2727 KiB  
Article
Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station
by Swati Bijlani, Ceth Parker, Nitin K. Singh, Maria A. Sierra, Jonathan Foox, Clay C. C. Wang, Christopher E. Mason and Kasthuri Venkateswaran
J. Fungi 2022, 8(2), 165; https://doi.org/10.3390/jof8020165 - 08 Feb 2022
Cited by 5 | Viewed by 5228
Abstract
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and [...] Read more.
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO2 conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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18 pages, 3968 KiB  
Article
Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment
by Ricardo Franco-Duarte, Neža Čadež, Teresa Rito, João Drumonde-Neves, Yazmid Reyes Dominguez, Célia Pais, Maria João Sousa and Pedro Soares
J. Fungi 2022, 8(1), 52; https://doi.org/10.3390/jof8010052 - 05 Jan 2022
Cited by 2 | Viewed by 2471
Abstract
Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora [...] Read more.
Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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Review

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16 pages, 335 KiB  
Review
Yeast Genomics and Its Applications in Biotechnological Processes: What Is Our Present and Near Future?
by Vivian Tullio
J. Fungi 2022, 8(7), 752; https://doi.org/10.3390/jof8070752 - 20 Jul 2022
Cited by 14 | Viewed by 3551
Abstract
Since molecular biology and advanced genetic techniques have become important tools in a variety of fields of interest, including taxonomy, identification, classification, possible production of substances and proteins, applications in pharmacology, medicine, and the food industry, there has been significant progress in studying [...] Read more.
Since molecular biology and advanced genetic techniques have become important tools in a variety of fields of interest, including taxonomy, identification, classification, possible production of substances and proteins, applications in pharmacology, medicine, and the food industry, there has been significant progress in studying the yeast genome and its potential applications. Because of this potential, as well as their manageability, safety, ease of cultivation, and reproduction, yeasts are now being extensively researched in order to evaluate a growing number of natural and sustainable applications to provide many benefits to humans. This review will describe what yeasts are, how they are classified, and attempt to provide a rapid overview of the many current and future applications of yeasts. The review will then discuss how yeasts—including those molecularly modified—are used to produce biofuels, proteins such as insulin, vaccines, probiotics, beverage preparations, and food additives and how yeasts could be used in environmental bioremediation and biocontrol for plant infections. This review does not delve into the issues raised during studies and research, but rather presents the positive outcomes that have enabled several industrial, clinical, and agricultural applications in the past and future, including the most recent on cow-free milk. Full article
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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