Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment

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.

Download Full-text

Effects of insecticides on adults and eggs of Drosophila suzukii (Diptera, Drosophilidae)

Revista Colombiana de Entomología ◽

10.25100/socolen.v43i2.5945 ◽

2017 ◽

Vol 43 (2) ◽

pp. 208 ◽

Cited By ~ 9

Author(s):

Daniele Cristine Hoffmann Schlesener ◽

Jutiane Wollmann ◽

Juliano De Bastos Pazini ◽

Anderson Dionei Grützmacher ◽

Flávio Roberto Mello Garcia

Keyword(s):

North America ◽

South America ◽

Chemical Control ◽

Stone Fruits ◽

Drosophila Suzukii ◽

Ovicidal Effect ◽

Mere Presence ◽

South Of Brazil ◽

Different Cultures ◽

First Time

Drosophila suzukii (Diptera, Drosophilidae) is an exotic species, endemic to Asia and currently a pest to small and stone fruits in several countries of North America and Europe. It was detected in 2013 for the first time in South America, in the south of Brazil. Unlike most drosophilids, this species deserves special attention, because the females are capable of oviposit inside healthy fruits, rendering their sale and export prohibited. Despite the confirmed existence of this species in different states of Brazil, this insect is yet been to be given the pest status. Nevertheless, the mere presence of this species is enough to cause concern to producers of small fruits and to justify further investigation for it’s control, especially chemical control for a possible change in status. Therefore, the goal of this work was to evaluate, in laboratory, mortality of D. suzukii adults and ovicidal effect when exposed to different insecticides registered for species of the Tephritidae and Agromyzidae families in different cultures. The insecticides deltamethrin, dimethoate, spinosad, fenitrothion, phosmet, malathion, methidathion, and zeta-cypermethrin resulted in mortality to 100 % of the subjects three days after the treatment (DAT). Regarding the effects over eggs, it was established that the insecticides fenitrothion, malathion, and methidathion deemed 100 % of the eggs not viable, followed by phosmet and diflubenzuron, which also caused elevated reduction in the eclosion of larvae two DAT.

Download Full-text

Mating of 2 Laboratory Saccharomyces cerevisiae Strains Resulted in Enhanced Production of 2-Phenylethanol by Biotransformation of L-Phenylalanine

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000455169 ◽

2017 ◽

Vol 27 (2) ◽

pp. 81-90 ◽

Cited By ~ 12

Author(s):

Jolanta Mierzejewska ◽

Aleksandra Tymoszewska ◽

Karolina Chreptowicz ◽

Kamil Krol

Keyword(s):

Saccharomyces Cerevisiae ◽

Batch Culture ◽

Fold Increase ◽

Biotechnological Production ◽

Aromatic Alcohol ◽

Enhanced Production ◽

Yeast Strains ◽

First Time

2-Phenylethanol (2-PE) is an aromatic alcohol with a rosy scent which is widely used in the food, fragrance, and cosmetic industries. Promising sources of natural 2-PE are microorganisms, especially yeasts, which can produce 2-PE by biosynthesis and biotransformation. Thus, the first challenging goal in the development of biotechnological production of 2-PE is searching for highly productive yeast strains. In the present work, 5 laboratory Saccharomyces cerevisiae strains were tested for the production of 2-PE. Thereafter, 2 of them were hybridized by a mating procedure and, as a result, a new diploid, S. cerevisiae AM1-d, was selected. Within the 72-h batch culture in a medium containing 5 g/L of <smlcap>L</smlcap>-phenylalanine, AM1-d produced 3.83 g/L of 2-PE in a shaking flask. In this way, we managed to select the diploid S. cerevisiae AM1-d strain, showing a 3- and 5-fold increase in 2-PE production in comparison to parental strains. Remarkably, the enhanced production of 2-PE by the hybrid of 2 yeast laboratory strains is demonstrated here for the first time.

Download Full-text

Experimental pieces of evidence for Mycobacterium ulcerans dormancy

10.1101/2020.08.27.269712 ◽

2020 ◽

Author(s):

A. Loukil ◽

R. Lalaoui ◽

H. Bogreau ◽

S. Regoui ◽

M. Drancourt ◽

...

Keyword(s):

Physiological State ◽

Nile Red ◽

Buruli Ulcer ◽

Ambient Air ◽

Opportunistic Pathogen ◽

Oxygen Depletion ◽

Mycobacterium Ulcerans ◽

Ecological Niches ◽

Intracellular Lipid ◽

First Time

ABSTRACTBackgroundWhether Mycobacterium ulcerans, the etiological agent of the neglected Buruli ulcer in numerous tropical countries, would exist in a dormant state as reported for closely related Mycobacterium species, is not established.MethodologySix M. ulcerans strains were exposed to a progressive depletion in oxygen for two months, using a previously described Wayne model of dormancy; and further examined by microscopy using DDD staining, microcalorimetry and subculture in the presence of dead and replicative M. ulcerans as controls.Principal Findings/ConclusionsM. ulcerans CU001 strain died during the progressive oxygen depletion and four of five remaining strains exhibited Nile Red-stained intracellular lipid droplets after DDD staining and a 14-20-day regrowth when exposed to ambient air, diagnosing dormancy. A fifth M. ulcerans 19423 strain stained negative in DDD and slowly regrew in 27 days. Three tested M. ulcerans strains yielded microcalorimetric pattern similar to that of the negative (dead) homologous controls, differing from that of the homologous positive (replicative) controls. The relevance of these experimental observations, suggesting a previously unreported dormancy state of M. ulcerans, needs to be investigated in the natural ecological niches where M. ulcerans thrive and in Buruli ulcer lesions.Author summaryMycobacterium ulcerans is an environmental opportunistic pathogen of mammals and humans, causing a subcutaneous necrotizing infection named Buruli ulcer. Molecular detection of M. ulcerans DNA revealed different ecological niches where M. ulcerans may thrive, but the molecular biology approach does not catch the physiological state of M. ulcerans in these different ecological niches. Thus, the reservoir and the mode of transmission of M. ulcerans remain elusive. Here, we investigated experimental dormancy of M. ulcerans by using a previously described Wayne model of dormancy coupled with microscopy using DDD staining, microcalorimetry and subculture. Our findings demonstrate for the first time that some M. ulcerans strains exhibit a physiological state of dormancy; potentially limiting isolation and culture of M. ulcerans from environmental niches.

Download Full-text

Genomic analysis of Landes goose origin goose hemorrhagic polyomavirus, China

10.22541/au.163251594.45640668/v1 ◽

2021 ◽

Author(s):

Ling Luo ◽

Xinglong Yu ◽

Xiang Qu ◽

Fei Zhao ◽

Yan Ding ◽

...

Keyword(s):

Causative Agent ◽

Mainland China ◽

Evolutionary Relationship ◽

Genomic Analysis ◽

Laboratory Diagnostics ◽

First Time ◽

Landes Geese ◽

Hatching Rates

A goose hemorrhagic polyomavirus (GHPV) outbreak occurred in a Goose Farm in Hunan, China, between January and July 2021. Approximately 1,500 breeding goose died, and hatching rates dropped from the previous 85% to about 50% in this outbreak. GHPV HUN-01, isolated from the liver of infected Landes geese, shared a close evolutionary relationship with the Toulouse Goose 2000 and 14234 strain, isolated from geese in France and Hungary. The isolation of GHPV from the livers of dead embryos also demonstrates that the virus can be transmitted vertically. In conclusion, clinical and laboratory diagnostics of the diseased geese in this outbreak were consistent with GHPV being the causative agent. We learned that this is the first time that GHPV has been isolated from geese in mainland China.

Download Full-text

DNA screening of Drosophila suzukii predators in berry field orchards shows new predatory taxonomical groups

PLoS ONE ◽

10.1371/journal.pone.0249673 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249673

Author(s):

Sara Sario ◽

Conceição Santos ◽

Fátima Gonçalves ◽

Laura Torres

Keyword(s):

Large Scale ◽

Field Studies ◽

Life Cycles ◽

Gut Content ◽

Drosophila Suzukii ◽

Potential Predator ◽

The Family ◽

First Time ◽

South Europe ◽

New Habitats

Drosophila suzukii (spotted wing drosophila, SWD) is a pandemic quarantine pest that attacks mostly red fruits. The high number of life cycles per year, its ability to rapidly invade and spread across new habitats, and highly polyphagous nature, makes this a particularly aggressive invasive species, for which efficient control methods are currently lacking. The use of native natural predators is particularly promising to anchor sustainable and efficient measures to control SWD. While several field studies have suggested the presence of potential predatory species in infested orchards, only a few confirmed the presence of SWD DNA in predators’ gut content. Here, we use a DNA-based approach to identify SWD predators among the arthropod diversity in South Europe, by examining the gut content of potential predator specimens collected in SWD-infested berry fields in North Portugal. These specimens were morphologically identified to the family/order, and their gut content was screened for the presence of SWD DNA using PCR. New SWD predatory taxonomical groups were identified, as Opiliones and Hemerobiidae, in addition to known SWD predators, such as Hemerobiidae, Chrysopidae, Miridae, Carabidae, Formicidae and Araneae. Additionally, the presence of a spider family, Uloboridae, in the orchards was recorded for the first time, posing this family as another SWD-candidate predator. This study sets important bases to further investigate the potential large-scale use of some of these confirmed predator taxa for SWD control in South Europe.

Download Full-text

Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

ISME Communications ◽

10.1038/s43705-021-00050-y ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Courtney M. Thomas ◽

Najwa Taib ◽

Simonetta Gribaldo ◽

Guillaume Borrel

Keyword(s):

Gut Microbiota ◽

Large Scale ◽

Genomic Analysis ◽

Host Adaptation ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Methyl Branch ◽

Mechanisms Of Adaptation ◽

Hydrogenotrophic Methanogens ◽

Almost All

AbstractOther than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.

Download Full-text

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma

Scientific Reports ◽

10.1038/s41598-019-52559-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 14

Author(s):

Xia Tang ◽

Delong Feng ◽

Min Li ◽

Jinxue Zhou ◽

Xiaoyuan Li ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Rna Seq ◽

Pairwise Interactions ◽

Micro Rnas ◽

Non Coding Rnas ◽

First Time

Abstract Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.

Download Full-text

Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

Scientific Reports ◽

10.1038/s41598-019-52209-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Safia Zeghbib ◽

Róbert Herczeg ◽

Gábor Kemenesi ◽

Brigitta Zana ◽

Kornélia Kurucz ◽

...

Keyword(s):

Geographical Location ◽

Data Sets ◽

Evolutionary Analysis ◽

Evolutionary Patterns ◽

Host Genus ◽

Evolution Analysis ◽

Zoonotic Viruses ◽

History Of ◽

First Time

Abstract Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

Download Full-text

Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production

FEMS Yeast Research ◽

10.1093/femsyr/foz034 ◽

2019 ◽

Vol 19 (4) ◽

Cited By ~ 3

Author(s):

Débora Trichez ◽

Andrei S Steindorff ◽

Carlos E V F Soares ◽

Eduardo F Formighieri ◽

João R M Almeida

Keyword(s):

Renewable Resources ◽

Xylose Reductase ◽

Genomic Analysis ◽

Product Yield ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Brazilian Cerrado ◽

Genome Sequences ◽

Yeast Strains ◽

Spathaspora Passalidarum

ABSTRACT Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.

Download Full-text

Disruptive ecological selection on a mating cue

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.1968 ◽

2012 ◽

Vol 279 (1749) ◽

pp. 4907-4913 ◽

Cited By ~ 97

Author(s):

Richard M. Merrill ◽

Richard W. R. Wallbank ◽

Vanessa Bull ◽

Patricio C. A. Salazar ◽

James Mallet ◽

...

Keyword(s):

Field Experiments ◽

Random Mating ◽

Experimental Manipulation ◽

Colour Pattern ◽

Disruptive Selection ◽

Ecological Niches ◽

Ecological Selection ◽

Wing Patterns ◽

Colour Patterns ◽

First Time

Adaptation to divergent ecological niches can result in speciation. Traits subject to disruptive selection that also contribute to non-random mating will facilitate speciation with gene flow. Such ‘magic’ or ‘multiple-effect’ traits may be widespread and important for generating biodiversity, but strong empirical evidence is still lacking. Although there is evidence that putative ecological traits are indeed involved in assortative mating, evidence that these same traits are under divergent selection is considerably weaker. Heliconius butterfly wing patterns are subject to positive frequency-dependent selection by predators, owing to aposematism and Müllerian mimicry, and divergent colour patterns are used by closely related species to recognize potential mates. The amenability of colour patterns to experimental manipulation, independent of other traits, presents an excellent opportunity to test their role during speciation. We conducted field experiments with artificial butterflies, designed to match natural butterflies with respect to avian vision. These were complemented with enclosure trials with live birds and real butterflies. Our experiments showed that hybrid colour-pattern phenotypes are attacked more frequently than parental forms. For the first time, we demonstrate disruptive ecological selection on a trait that also acts as a mating cue.

Download Full-text