scholarly journals Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

2019 ◽  
Vol 7 (11) ◽  
pp. 489 ◽  
Author(s):  
Ievgeniia A. Tiukova ◽  
Huifeng Jiang ◽  
Jacques Dainat ◽  
Marc P. Hoeppner ◽  
Henrik Lantz ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Biotechnological Applications ◽  
Genetic Determinants ◽  
Alcohol Content ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
High Attenuation ◽  
Spoilage Yeast ◽  
Functional Genome Annotation ◽  
Low Alcohol

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

2017 ◽  
Vol 27 (3) ◽  
pp. 147-158 ◽  
Author(s):  
Liliana Godoy ◽  
Evelyn Silva-Moreno ◽  
Wladimir Mardones ◽  
Darwin Guzman ◽  
Francisco A. Cubillos ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Survival Strategies ◽  
Whole Genome ◽  
Biotechnological Applications ◽  
Genome Sequences ◽  
Wine Production ◽  
Brettanomyces Bruxellensis ◽  
Biotechnological Potential ◽  
Spoilage Yeast ◽  
Genome Comparisons

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to <i>Brettanomyces bruxellensis </i>contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 <i>B. bruxellensis </i>annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of <i>B. bruxellensis</i> LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of <i>B. bruxellensis</i> LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of <i>B. bruxellensis</i> LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast <i>B. bruxellensis</i>.

scholarly journals Insights into the Genome Sequence ofChromobacterium amazonenseIsolated from a Tropical Freshwater Lake

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Alexandre Bueno Santos ◽  
Patrícia Silva Costa ◽  
Anderson Oliveira do Carmo ◽  
Gabriel da Rocha Fernandes ◽  
Larissa Lopes Silva Scholte ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Diversity ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
Draft Assembly ◽  
Functional Studies ◽  
Alpha Hemolysin ◽  
Type Iv ◽  
Nudix Hydrolases ◽  
Colicin V

Members of the genusChromobacteriumhave been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis ofChromobacterium amazonensestrain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike otherChromobacteriumspecies, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of theC. amazonensestrain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involvingChromobacterium-related isolates and improves our understanding of the global genomic diversity ofChromobacteriumspecies.

scholarly journals Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

2021 ◽  
Author(s):  
Marco Alexandre Guerreiro ◽  
Steven Ahrendt ◽  
Jasmyn Pangilinan ◽  
Cindy Chen ◽  
Mi Yan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Cell Wall ◽  
Draft Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
Pheromone Receptor ◽  
Genes Encoding ◽  
Cryptococcus Species ◽  
Mat Locus

Abstract The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. Additionally, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

scholarly journals Low-Alcohol Wine: A Narrative Review on Consumer Perception and Behaviour

Beverages ◽  
2018 ◽  
Vol 4 (4) ◽  
pp. 82 ◽  
Author(s):  
Tamara Bucher ◽  
Kristine Deroover ◽  
Creina Stockley
Keyword(s):  
Alcohol Consumption ◽  
Narrative Review ◽  
Consumer Perception ◽  
Alcohol Content ◽  
Wine Consumption ◽  
Reduce Alcohol Consumption ◽  
Alcohol Related Harm ◽  
Low Alcohol ◽  
Related Harm

Low- and reduced-alcohol beverages become increasingly popular in many countries with different factors driving a change in the beverage market. The aim of the current narrative review is (a) to provide an introduction on low-alcohol wine, and (b) to provide an overview of the literature on research that investigated perception and behaviour related to low-alcohol wine consumption. Wines with reduced alcohol content can be an interesting product for a variety of stakeholders and may offer benefits for consumers while having the potential to reduce alcohol consumption and therefore contribute to the reduction of alcohol-related harm. Additional research and marketing efforts are needed to further increase awareness of the availability and quality of these products.

scholarly journals Predicting Coding Potential from Genome Sequence: Application to Betaherpesviruses Infecting Rats and Mice

2005 ◽  
Vol 79 (12) ◽  
pp. 7570-7596 ◽  
Author(s):  
Luciano Brocchieri ◽  
Thomas N. Kledal ◽  
Samuel Karlin ◽  
Edward S. Mocarski
Keyword(s):  
Genome Annotation ◽  
Mrna Splicing ◽  
Overlapping Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Coding Regions ◽  
Translation Signals ◽  
Rats And Mice ◽  
Coding Potential ◽  
Exon Gene

ABSTRACT Prediction of protein-coding regions and other features of primary DNA sequence have greatly contributed to experimental biology. Significant challenges remain in genome annotation methods, including the identification of small or overlapping genes and the assessment of mRNA splicing or unconventional translation signals in expression. We have employed a combined analysis of compositional biases and conservation together with frame-specific G+C representation to reevaluate and annotate the genome sequences of mouse and rat cytomegaloviruses. Our analysis predicts that there are at least 34 protein-coding regions in these genomes that were not apparent in earlier annotation efforts. These include 17 single-exon genes, three new exons of previously identified genes, a newly identified four-exon gene for a lectin-like protein (in rat cytomegalovirus), and 10 probable frameshift extensions of previously annotated genes. This expanded set of candidate genes provides an additional basis for investigation in cytomegalovirus biology and pathogenesis.

Prevention of alcohol-related violence

1998 ◽  
Vol 25 (3) ◽  
pp. 477-509 ◽  
Author(s):  
Kai Pernanen
Keyword(s):  
Public Health ◽  
Alcohol Intoxication ◽  
Public Health Problem ◽  
Prevention Programs ◽  
Cultural Factors ◽  
Alcohol Problems ◽  
Alcohol Content ◽  
High Risk Factors ◽  
Specific Factors ◽  
Low Alcohol

Four target areas in the prevention of alcohol-related violence are discussed: alcohol-specific, individual, situational and (sub)cultural factors. Important alcohol-specific factors are those determining the prevalence and duration of intoxication events in the population. Traditional prevention of alcohol problems aims to cut down overall alcohol use and/or favors beverages of low alcohol content. More specific prevention programs would locate individuals who are highly violence-prone under alcohol intoxication and specify characteristics of situations and (sub)cultures that are conducive to alcohol-related violence. Presently prevention of bar violence targets the widest range of high-risk factors. Prevention of alcohol-related conflicts and escalation to violence in interactional situations is perhaps the least systematically developed area. The recent emphasis on violence as a public health problem has brought forth new prevention programs. Studying how these general programs affect alcohol-related violence and coordinating the two types of efforts will be a key task for the future.

scholarly journals Use of Average Mutual Information and Derived Measures to Find Coding Regions

Entropy ◽  
2021 ◽  
Vol 23 (10) ◽  
pp. 1324
Author(s):  
Garin Newcomb ◽  
Khalid Sayood
Keyword(s):  
Mutual Information ◽  
Genome Annotation ◽  
High Accuracy ◽  
Gene Identification ◽  
Coding Region ◽  
Average Mutual Information ◽  
Protein Coding ◽  
Noncoding Sequences ◽  
Coding Regions ◽  
Genomic Regions

One of the important steps in the annotation of genomes is the identification of regions in the genome which code for proteins. One of the tools used by most annotation approaches is the use of signals extracted from genomic regions that can be used to identify whether the region is a protein coding region. Motivated by the fact that these regions are information bearing structures we propose signals based on measures motivated by the average mutual information for use in this task. We show that these signals can be used to identify coding and noncoding sequences with high accuracy. We also show that these signals are robust across species, phyla, and kingdom and can, therefore, be used in species agnostic genome annotation algorithms for identifying protein coding regions. These in turn could be used for gene identification.

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