De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel

Transcriptomic investigation of the interaction between a biocontrol yeast, Papiliotrema terrestris strain PT22AV, and the postharvest fungal pathogen Penicillium expansum on apple

Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) Papiliotrema terrestris, the pathogen Penicillium expansum, and the host Malus domestica. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissue, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to P. expansum analysis, 1017 DEGs are upregulated when grown in apple tissue, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host M. domestica finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with P. expansum. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.

PpMYB1 and PpNPR1 interact to enhance the resistance of peach fruit to Rhizopus stolonifer infection

MYB transcription factors play important role in stress-resistance of plants. Nevertheless, the function of MYB TFs in peach Rhizopus rot remains poorly understood. Herein, Pichia guilliermondii treatment activated resistance against Rhizopus stolonifer, as illustrated by reductions in the incidence rate and severity of Rhizopus rot disease, increased enzyme activities and gene expression of chitinase (CHI) and β-1,3-glucanase (GLU), and enhancement of energy production by inducing the activities and expression of H⁺-ATPase and Ca²⁺-ATPase, succinate dehydrogenase (SDH), and cytochrome c oxidase (CCO). Moreover, an R1-type MYB, PpMYB1, from peach fruit was induced during R. stolonifer infection and in response to P. guilliermondii treatment. PpMYB1 activated the transcription of PpCHI-EP3 and PpGLU-like genes and the energy metabolism-related gene PpH⁺-ATPase1 by directly targeting the MBS element. Importantly, PpMYB1 interacted with PpNPR1 to form a heterodimer, which was conducive to enhancing the activation of target gene transcription. Collectively, our findings suggest that PpMYB1 cooperates with PpNPR1 to positively regulate disease resistance by activating the disease defense system and energy metabolism in peaches.

The Role of ABA in the Interaction between Citrus Fruit and Penicillium digitatum

Abscisic acid (ABA) protects citrus fruit against Penicillium digitatum infection. The global mechanisms involved in the role of ABA in the P. digitatum-citrus fruit interaction are unknown. Here, we determine the transcriptome differences between the Navelate (Citrus sinensis (L.) Osbeck) orange and its ABA-deficient mutant Pinalate, which is less resistant to infection. Low ABA levels may affect both the constitutive mechanisms that protect citrus fruit against P. digitatum and early responses to infection. The repression of terpenoid, phenylpropanoid and glutation metabolism; of oxidation-reduction processes; and of processes related to the defense response to fungus and plant hormone signal transduction may be one part of the constitutive defense reduced in the mutant against P. digitatum. Our results also provide potential targets for developing P. digitatum-citrus fruit-resistant varieties. Of those up-regulated by ABA, a thaumatin protein and a bifunctional inhibitor/LTP, which are relevant in plant immunity, were particularly remarkable. It is also worth highlighting chlorophyllase 1 (CLH1), induced by infection in Pinalate, and the OXS3 gene, which was down-regulated by ABA, because the absence of OXS3 activates ABA-responsive genes in plants.

The Role of Plasma Membrane Pleiotropic Drug Resistance Transporters in the Killer Activity of Debaryomyces hansenii and Wickerhamomyces anomalus Toxins

The killer strains of Debaryomyces hansenii and Wickerhamomyces anomalus species secrete antimicrobial proteins called killer toxins which are active against selected fungal phytopathogens. In our research, we attempted to investigate the role of plasma membrane pleiotropic drug resistance (PDR) transporters (Pdr5p and Snq2p) in the mechanism of defense against killer toxins. Saccharomyces cerevisiae mutant strains with strengthened or weakened pleiotropic drug resistance due to increased or reduced number of mentioned PDR efflux pumps were tested for killer toxin susceptibility. The present study demonstrates the influence of the Snq2p efflux pump in immunity to W.anomalus BS91 killer toxin. It was also shown that the activity of killer toxins of D. hansenii AII4b, KI2a, MI1a and CBS767 strains is regulated by other transporters than those influencing W. anomalus killer toxin activity. In turn, this might be related to the functioning of the Pdr5p transporter and a complex cross-talk between several regulatory multidrug resistance networks. To the best of our knowledge, this is the first study that reports the involvement of PDR transporters in the cell membrane of susceptible microorganisms in resistance to killer yeasts’ toxins.

The whole-genome sequence of the novel yeast species Metschnikowia persimmonesis isolated from medicinal plant Diospyros kaki Thunb

The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high-quality whole-genome assembly of M. persimmonesis produced by PacBio RS II sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7029 genes and 6939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities, M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

Influence of arginine on the biocontrol efficiency of Metschnikowia citriensis against Geotrichum citri-aurantii causing sour rot of postharvest citrus fruit

This study investigated the effect of arginine (Arg) on the antagonistic activity of Metschnikowia citriensis against sour rot caused by Geotrichum citri-aurantii in postharvest citrus, and evaluated the possible mechanism therein. Arg treatment up-regulated the PUL genes expression, and significantly induced the pulcherriminic acid (PA) production of M. citriensis, which related to the capability of iron depletion of M. citriensis. By comparing the biocontrol effects of Arg-treated and untreated yeast cells, it was found that Arg treatment significantly enhanced the biocontrol efficacy of M. citriensis, and 5 mmol L^-1 Arg exerted the best effect. Additionally, the biofilm formation ability of M. citriensis was greatly enhanced by Arg, and the higher population density of yeast cells in citrus wounds was also observed in Arg treatment groups stored both at 25 °C and 4 °C. Moreover, Arg was shown to function as a cell protectant to elevate antioxidant enzyme activity [including catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPX)] and intracellular trehalose content to resist oxidative stress damage, that directly helped to enhance colonization ability of yeasts in fruit wounds. These results suggest the application of Arg is a useful approach to improve the biocontrol performance of M. citriensis.

Albedo- and Flavedo-Specific Transcriptome Profiling Related to Penicillium digitatum Infection in Citrus Fruit

Penicillium digitatum is the main postharvest pathogen of citrus fruit. Although the inner fruit peel part (albedo) is less resistant than the outer part (flavedo) to P. digitatum, the global mechanisms involved in their different susceptibility remain unknown. Here, we examine transcriptome differences between both tissues at fruit harvest and in their early responses to infection. At harvest, not only was secondary metabolism, involving phenylpropanoids, waxes, and terpenoids, generally induced in flavedo vs. albedo, but also energy metabolism, transcription factors (TFs), and biotic stress-related hormones and proteins too. Flavedo-specific induced responses to infection might be regulated in part by ERF1 TF, and are related to structural plant cell wall reinforcement. Other induced responses may be related to H₂O₂, the synthesis of phenylpropanoids, and the stress-related proteins required to maintain basal defense responses against virulent pathogens, whereas P. digitatum represses some hydrolase-encoding genes that play different functions and auxin-responsive genes in this peel tissue. In infected albedo, the repression of transport and signal transduction prevail, as does the induction of not only the processes related to the synthesis of flavonoids, indole glucosinolates, cutin, and oxylipins, but also the specific genes that elicit plant immunity against pathogens.

Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.

Potential of microbial endophytes to enhance the resistance to postharvest diseases of fruit and vegetables

Food loss of fruit and vegetables caused by postharvest diseases is a major issue worldwide. The method used to prevent and control postharvest diseases is usually to use chemical fungicides, but long-term and large-scale use will make the pathogens resistant and potentially have a negative impact on human health and the ecological environment. Therefore, finding a safe and effective biological control method instead of chemical control is a hot research topic in recent years. Endophytes, colonizing plants asymptomatically, can promote the growth of the hosts and enhance their resistance. The use of endophytes as biological control agents for postharvest diseases of fruit and vegetables has attracted increasing attention in the last 20 years. Compared with chemical control, endophytes have the advantages of being more environmentally friendly, sustainable, and safer. However, there are relatively few relevant studies, so herein we summarize the available literature. This review focuses mainly on the recent progress of using endophytes to enhance the resistance of postharvest fruit and vegetables to diseases, with the emphasis on the possible mechanisms and the potential applications. Furthermore, this article suggests future areas for study using antagonistic endophytes to prevent and control fruit and vegetable postharvest diseases: (i) screening more potential broad-spectrum anti-pathogen endophytes and their metabolic active substances by the method of macrogenomics; (ii) elucidating the underlining molecular mechanism among endophytes, harvested vegetables and fruit, pathogens, and microbial communities; (iii) needing more application research to overcome the difficulties of commercialization practice. © 2020 Society of Chemical Industry.

Variation among Metschnikowia pulcherrima Isolates for Genetic Modification and Homologous Recombination

Metschnikowia pulcherrima is a non-conventional yeast with the potential to be used in biotechnological processes, especially involving low-cost feedstock exploitation. However, there are a lack of tools for researching it at a molecular level and for producing genetically modified strains. We tested the amenability to genetic modification of ten different strains, establishing a transformation protocol based on LiAc/PEG that allows us to introduce heterologous DNA. Non-homologous integration was broadly successful and homologous recombination was successful in two strains. Chemical inhibition of non-homologous end joining recombination had a modest effect on the improvement of homologous recombination rates. Removal of selective markers via flippase recombinase was successful across integrated loci except for those targeted to the native URA3 locus, suggesting that the genome sequence or structure alters the efficacy of this system.

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

The full-length single-molecular sequencing and short reads Illumina sequencing were combined to generate the transcripts of adzuki bean with high-quality. A total of 17,636 loci and 60,454 transcripts were detected in this study. To characterize the drought-responsive genes during seed germination in adzuki bean, two varieties, i.e., tolerant and sensitive to drought stress, were selected to conduct analysis of alternative splicing dynamics (AS) and differentially expressed genes (DEGs) by combining the newly assembled draft genome and public adzuki bean reference genome. AS analysis indicated that both the two varieties underwent a little more AS events under control conditions than under drought stress. Among the AS events, IR (intron retention) predominately accounted for 34.3%, whereas AD (alternative donor site) was the least frequent with 15.8%. Meanwhile, 562 long non-coding RNAs, 409 fusion genes and 1208 transcription factors were identified. Moreover, a total of 5,337 DEGs were identified in comparison of the two varieties with drought or control treatments. Notably, 82 DEGs were discovered in the two varieties under drought stress, which might be the candidate in regulation of seed germination to answer for different drought tolerance. The DEGs encoded proteins involved in primary or second metabolism, plant hormone signal transduction, transcript or translation processes, ubiquitin proteasome system, transcription factor, transporters, and so on. The results facilitate to increase the knowledge about the mechanism of drought tolerance during crop seed germination, and provide reference for the breeding of drought-tolerant adzuki bean.

The Genus Metschnikowia in Enology

Over the last decade, several non-Saccharomyces species have been used as an alternative yeast for producing wines with sensorial properties that are distinctive in comparison to those produced using only Saccharomycescerevisiae as the classical inoculum. Among the non-Saccharomyces wine yeasts, Metschnikowia is one of the most investigated genera due to its widespread occurrence and its impact in winemaking, and it has been found in grapevine phyllospheres, fruit flies, grapes, and wine fermentations as being part of the resident microbiota of wineries and wine-making equipment. The versatility that allows some Metschnikowia species to be used for winemaking relies on an ability to grow in combination with other yeast species, such as S. cerevisiae, during the first stages of wine fermentation, thereby modulating the synthesis of secondary metabolites during fermentation in order to improve the sensory profile of the wine. Metschnikowia exerts a moderate fermentation power, some interesting enzymatic activities involving aromatic and color precursors, and potential antimicrobial activity against spoilage yeasts and fungi, resulting in this yeast being considered an interesting tool for use in the improvement of wine quality. The abovementioned properties have mostly been determined from studies on Metschnikowia pulcherrima wine strains. However, M. fructicola and M. viticola have also recently been studied for winemaking purposes.

Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism

Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the exact taxonomic position of the strains is hampered by the shortage of distinctive morphological and physiological properties of the species of the clade and the lack of rDNA barcode gaps. The rDNA repeats of the type strains of the species are not homogenized and are assumed to evolve by a birth-and-death mechanism combined with reticulation. The taxonomic division is further hampered by the incomplete biological (reproductive) isolation of the species: certain type strains can be hybridized and genome sequencing revealed chimeric genome structures in certain strains that might have evolved from interspecies hybrids (alloploid genome duplication). Various mechanisms have been proposed for the antimicrobial antagonism. One is related to pulcherrimin production. The diffusible precursor of pulcherrimin, the pulcherriminic acid is secreted by the cells into the environment where it forms the insoluble pulcherrimin with the ferric ions. The lack of free iron caused by the immobilization of ferric ions inhibits the growth of many microorganisms. Recent results of research into the complexity of the taxonomic division of the pulcherrimin-producing Metschnikowia yeasts and the mechanism(s) underlying their antimicrobial antagonism are discussed in this review.

Biocontrol yeasts: mechanisms and applications

Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.

Role of biological control agents and physical treatments in maintaining the quality of fresh and minimally-processed fruit and vegetables

Fruit and vegetables are an important part of human diets and provide multiple health benefits. However, due to the short shelf-life of fresh and minimally-processed fruit and vegetables, significant losses occur throughout the food distribution chain. Shelf-life extension requires preserving both the quality and safety of food products. The quality of fruit and vegetables, either fresh or fresh-cut, depends on many factors and can be determined by analytical or sensory evaluation methods. Among the various technologies used to maintain the quality and increase shelf-life of fresh and minimally-processed fruit and vegetables, biological control is a promising approach. Biological control refers to postharvest control of pathogens using microbial cultures. With respect to application of biological control for increasing the shelf-life of food, the term biopreservation is favored, although the approach is identical. The methods for screening and development of biocontrol agents differ greatly according to their intended application, but the efficacy of all current approaches following scale-up to commercial conditions is recognized as insufficient. The combination of biological and physical methods to maintain quality has the potential to overcome the limitations of current approaches. This review compares biocontrol and biopreservation approaches, alone and in combination with physical methods. The recent increase in the use of meta-omics approaches and other innovative technologies, has led to the emergence of new strategies to increase the shelf-life of fruit and vegetables, which are also discussed herein.

Potential of Yeasts as Biocontrol Agents of the Phytopathogen Causing Cacao Witches' Broom Disease: Is Microbial Warfare a Solution?

Plant diseases caused by fungal pathogens are responsible for major crop losses worldwide, with a significant socio-economic impact on the life of millions of people who depend on agriculture-exclusive economy. This is the case of the Witches’ Broom Disease (WBD) affecting cacao plant and fruit in South and Central America. The severity and extent of this disease is prospected to impact the growing global chocolate market in a few decades. WBD is caused by the basidiomycete fungus Moniliophthora perniciosa. The methods used to contain the fungus mainly rely on chemical fungicides, such as copper-based compounds or azoles. Not only are these highly ineffective, but also their utilization is increasingly restricted by the cacao industry, in part because it promotes fungal resistance, in part related to consumers’ health concerns and environmental awareness. Therefore, the disease is being currently tentatively controlled through phytosanitary pruning, although the full removal of infected plant material is impossible and the fungus maintains persistent inoculum in the soil, or using an endophytic fungal parasite of Moniliophthora perniciosa which production is not sustainable. The growth of Moniliophthora perniciosa was reported as being antagonized in vitro by some yeasts, which suggests that they could be used as biological control agents, suppressing the fungus multiplication and containing its spread. Concurrently, some yeast-based products are used in the protection of fruits from postharvest fungal spoilage, and the extension of diverse food products shelf-life. These successful applications suggest that yeasts can be regarded a serious alternative also in the pre-harvest management of WBD and other fungal plant diseases. Yeasts’ GRAS (Generally Recognized as Safe) nature adds to their appropriateness for field application, not raising major ecological concerns as do the present more aggressive approaches. Importantly, mitigating WBD, in a sustainable manner, would predictably have a high socioeconomic impact, contributing to diminish poverty in the cacao-producing rural communities severely affected by the disease. This review discusses the importance/advantages and the challenges that such a strategy would have for WBD containment, and presents the available information on the molecular and cellular mechanisms underlying fungi antagonism by yeasts.

Stress-Tolerant Yeasts: Opportunistic Pathogenicity Versus Biocontrol Potential

Stress-tolerant fungi that can thrive under various environmental extremes are highly desirable for their application to biological control, as an alternative to chemicals for pest management. However, in fungi, the mechanisms of stress tolerance might also have roles in mammal opportunism. We tested five species with high biocontrol potential in agriculture (Aureobasidium pullulans, Debayomyces hansenii, Meyerozyma guilliermondii, Metschnikowia fructicola, Rhodotorula mucilaginosa) and two species recognized as emerging opportunistic human pathogens (Exophiala dermatitidis, Aureobasidium melanogenum) for growth under oligotrophic conditions and at 37 °C, and for tolerance to oxidative stress, formation of biofilms, production of hydrolytic enzymes and siderophores, and use of hydrocarbons as sole carbon source. The results show large overlap between traits desirable for biocontrol and traits linked to opportunism (growth under oligotrophic conditions, production of siderophores, high oxidative stress tolerance, and specific enzyme activities). Based on existing knowledge and these data, we suggest that oligotrophism and thermotolerance together with siderophore production at 37 °C, urease activity, melanization, and biofilm production are the main traits that increase the potential for fungi to cause opportunistic infections in mammals. These traits should be carefully considered when assessing safety of potential biocontrol agents.

Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing

Drought and salinity are the major factors that limit the faba bean (Vicia faba L.) production worldwide. The aim of this study is to identify the water stress differentially expressed genes (DEGs) through the root transcriptome analyses of the drought-tolerant Hassawi 2 genotype at vegetative and flowering stages. A total of 624.8 M high-quality Illumina reads were generated and assembled into 198,155 all-unigenes with a mean length of 738 bp and an N50 length of 1347 bp. Among all-unigenes, 78,262 were assigned to non-redundant (Nr), 66,254 to nucleotide (Nt), 54,034 to KEGG, and 43,913 to gene ontology (GO) annotations. A total of 36,834 and 35,510 unigenes were differentially expressed at the vegetative and flowering stages of Hassawi 2 under drought stress, respectively. The majority of unigenes were down-regulated at both developmental stages. However, the number of genes up-regulated (15,366) at the flowering stage exceeded the number of those up-regulated (14,097) at the vegetative stage, and the number of genes down-regulated (20,144) at the flowering stage was smaller than the number of those down-regulated (22,737) at the vegetative stage. The drought stress-responsive differentially expressed unigenes coded for various regulatory proteins, including protein kinases and phosphatases, transcription factors and plant hormones and functional proteins including enzymes for osmoprotectant, detoxification and transporters were differentially expressed, most of which were largely up-regulated. Moreover, a substantial proportion of the DEGs identified in this study were novel, most exhibited a significant change in their expression levels under water stress, making them an unexploited resource that might control specific responses to drought stress in the faba bean. Finally, qRT-PCR results were found almost consistent with the results of next-generation sequencing. Our data will help in understanding the drought tolerance mechanisms in plants and will provide resources for functional genomics.

Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127

Metschnikowia strain UCD127 was isolated from soil in Ireland and sequenced. It is a highly heterozygous diploid strain with 385,000 single nucleotide polymorphisms (SNPs). Its ribosomal DNA has the highest similarity to that of M. chrysoperlae, but its ACT1 and TEF1 loci and mitochondrial genome show affinity to those of M. fructicola, whose genome is significantly larger.

Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases

The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other three available closely related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue.

Genetic basis of priority effects: insights from nectar yeast

Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we de novo assembled the genome of the nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds and complete mitochondrion, with gap-free coverage over gene spaces. We found a high rate of tandem gene duplication in this genome, enriched for nitrogen metabolism and transport. Both high-capacity amino acid importers, GAP1 and PUT4, present as tandem gene arrays, were highly expressed in synthetic nectar and regulated by the availability and quality of amino acids. In experiments with competitive nectar yeast, Candida rancensis, amino acid addition alleviated suppression of C. rancensis by early arrival of M. reukaufii, corroborating that amino acid scavenging may contribute to priority effects. Because niche pre-emption via rapid resource depletion may underlie priority effects in a broad range of microbial, plant and animal communities, nutrient scavenging genes like the ones we considered here may be broadly relevant to understanding priority effects.

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.

Potential Role of Exoglucanase Genes (WaEXG1 and WaEXG2) in the Biocontrol Activity of Wickerhamomyces anomalus

The use of yeasts, including Wickerhamomyces anomalus, as biocontrol agents of fungi responsible for postharvest diseases of fruits and vegetables has been investigated for the past two decades. Among a variety of mechanisms, the production of glucanases coded by the "killer genes" WaEXG1 and WaEXG2 have been reported to play a role in the ability of yeast to inhibit other fungi. The objective of the present study was to determine the expression of these genes by RT-qPCR, utilizing gene-specific primers, when W. anomalus was grown on grape berries and oranges that were either non-inoculated or inoculated with Botrytis cinerea or Penicillium digitatum, or in minimal media supplemented with cell walls of various plant pathogens and different amounts of glucose. Results indicated that WaEXG2 was more responsive than WaEXG1 to the nutritional environment (including the addition of glucose to cell wall-amended media) in vitro and appeared to play a greater role in the cellular metabolism of W. anomalus. WaEXG2 expression also appeared to be more responsive to the presence of cell walls of P. digitatum and B. cinerea than other fungal species, whereas the same level of induction was not seen in vivo when the yeast was grown in wounded/pathogen-inoculated fruits.

Transcriptional profiling analysis of Penicillium digitatum, the causal agent of citrus green mold, unravels an inhibited ergosterol biosynthesis pathway in response to citral

Background

Green mold caused by Penicillium digitatum is the most damaging postharvest diseases of citrus fruit. Previously, we have observed that citral dose-dependently inhibited the mycelial growth of P. digitatum, with the minimum inhibitory concentration (MIC) of 1.78 mg/mL, but the underlying molecular mechanism is barely understood.

Results

In this study, the transcriptional profiling of the control and 1/2MIC-citral treated P. digitatum mycelia after 30 min of exposure were analyzed by RNA-Seq. A total of 6355 genes, including 2322 up-regulated and 4033 down-regulated genes, were found to be responsive to citral. These genes were mapped to 155 KEGG pathways, mainly concerning mRNA surveillance, RNA polymerase, RNA transport, aminoacyl-tRNA biosynthesis, ABC transporter, glycolysis/gluconeogenesis, citrate cycle, oxidative phosphorylation, sulfur metabolism, nitrogen metabolism, inositol phosphate metabolism, fatty acid biosynthesis, unsaturated fatty acids biosynthesis, fatty acid metabolism, and steroid biosynthesis. Particularly, citral exposure affected the expression levels of five ergosterol biosynthetic genes (e.g. ERG7, ERG11, ERG6, ERG3 and ERG5), which corresponds well with the GC-MS results, the reduction in ergosterol content, and accumulation of massive lanosterol. In addition, ERG11, the gene responsible for lanosterol 14α-demethylase, was observed to be the key down-regulated gene in response to citral.

Conclusion

Our present finding suggests that citral could exhibit its antifungal activity against P. digitatum by the down-regulation of ergosterol biosynthesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2943-4) contains supplementary material, which is available to authorized users.

Yeasts isolated from figs (Ficus carica L.) as biocontrol agents of postharvest fruit diseases

Fresh fruit is highly perishable during postharvest life, mainly due to fungal growth. Thus, fungal control is an important goal for the fruit industry. In this work, a selection of antagonistic yeasts isolated from fig and breba crops were screened in vitro. The isolated yeasts were challenged with three moulds isolated from decayed figs and breba crops, identified as Penicillium expansum M639 and Cladosporium cladosporioides M310 and M624, and pathogenic moulds Botrytis cinerea CECT20518 and Monilia laxa CA1 from culture collections. Two yeast isolates, Hanseniaspora opuntiae L479 and Metschnikowia pulcherrima L672, were selected for their ability to inhibit the growth of aforementioned moulds. These yeasts reduced the radial growth of moulds on PDA by between 45.23% and 66.09%. Antagonistic activity was associated with the interaction of live yeast cells with moulds. M. pulcherrima L672 apparently parasitised C. cladosporioides isolates. In addition, challenges were assayed using wounded apples and nectarines, with significant reductions in percent infection and lesion size for all moulds tested. To our knowledge, this is the first report identifying H. opuntiae as an antagonist against different pathogenic moulds.

Comparative transcriptional profiling of orange fruit in response to the biocontrol yeast Kloeckera apiculata and its active compounds

Background

The yeast Kloeckera apiculata strain 34–9 is an antagonist that shows biological control activity against the postharvest fungal pathogens of citrus. An antifungal compound, 2-phenylethanol (PEA), has been identified from the extract of K. apiculata. To better understand the molecular processes underlying the response of citrus fruit tissue to K. apiculata, the extract and PEA, microarray analyses were performed on navel oranges using an Affymetrix Citrus GeneChip.

Results

As many as 801, 339 and 608 differentially expressed genes (DEGs) were identified after the application of K. apiculata, the extract and PEA, respectively. In general, K. apiculata induced the expression of defence-related genes. In addition to chitinase and β-1,3-glucanase, genes involved in ethylene (ET), jasmonic acid (JA), calcium signalling, MAPK signalling and phenylalanine metabolism were induced. In contrast, monodehydroascorbate reductase, superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and carotenoid biosynthesis genes were down-regulated. The expression profiles for the extract- and PEA-treated samples were similar to that found for yeast (sharing 57.4 % DEGs), with a significant increase in the transcript levels of defence-related genes.

Conclusion

This study provides a global picture of the gene expression changes in navel oranges after the application of the antagonist yeast K. apiculata, its extract and PEA. The interpretation of the DEGs revealed new insight into the molecular processes that regulate the defence responses in orange tissue.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2333-3) contains supplementary material, which is available to authorized users.

Genomics and the making of yeast biodiversity

Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.

Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms

Background

Penicillium digitatum is one of the most destructive postharvest pathogen of citrus fruits, causing fruit decay and economic loss. The emergence of fungicide-resistant strains made the control of P. digitatum more difficult. While the genome of P. digitatum is available, there has been few reports about its resistant mechanism from the transcriptome perspective and there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.

Methods

Total RNA of P. digitatum strain HS-F6 (prochloraz-resistant strain) and HS-E3 (prochloraz-susceptible strain) before and after prochloraz-treatment were extracted and sequenced on an Illumina Hiseq 2000 platform. The transcriptome data of four samples were compared and analyzed using differential expression analysis, novel transcripts prediction and alternative splicing analysis, SNP analysis and quantitative real-time PCR.

Results

We present a large scale analysis about the transcriptome data of P. digitatum. The whole RNA was extracted from a prochloraz-resistant strain (HS-F6) and a prochloraz-susceptible strain (HS-E3) before and after prochloraz-treatment and sequenced by Illumina technology. A total of more than 100 million reads were generated and de novo assembled into 9760 transcripts that contained annotated genes after quality control and sequence assembling. 6625 single nucleotide variations (SNVs) were identified from the sequences aligned against the reference genome. Gene expression profiling analysis was performed upon prochloraz treatment in HS-F6 and HS-E3, and differential expression analysis was used to identify genes related to prochloraz-response and drug-resistance: there are 224 differentially expressed genes in HS-E3 and 1100 differentially expressed genes in HS-F6 after prochloraz-treatment. Moreover, gene expression profile in prochloraz-resistant strain HS-F6 is quite different from that in HS-E3 before prochloraz-treatment, 1520 differential expression genes were identified between the two strains. Gene ontology (GO) term enrichment and KEGG enrichment were then performed to classify the differential expression genes. Among these genes, there are a lot of transporter encoding genes including 14 MFS (Major Facilitator Superfamily) transporters, 8 ABC (ATP-binding cassette transporter) and 3 MATE (multidrug and toxic compound extrusion family) transporters. Meanwhile, the roles of typical MFS, ABC and MATE proteins in prochloraz resistance were investigated using real-time quantitative PCR.

Conclusions

The sequencing-based transcriptome data of P. digitatum demonstrate differences between prochloraz-resistant and prochloraz-susceptible strains with prochloraz-treatment. The differences existed in expressed transcripts, splice isoforms and GO categories, which would contribute to our knowledge on the molecular mechanisms involved in drug resistance of P. digitatum.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2043-x) contains supplementary material, which is available to authorized users.

Transcriptome analysis of the pearl oyster (Pinctada fucata) hemocytes in response to Vibrio alginolyticus infection

The pearl oyster Pinctada fucata is cultured widely for production of marine pearls in China, while mass mortalities, likely related to pathogenic infections, have occurred frequently in juvenile, mother and operated oysters. To address this issue, understanding host defense mechanisms of P. fucata against pathogenic challenge is extremely important. In the present study, a comparative analysis of hemocyte transcriptomes of P. fucata before and after Vibrio alginolyticus infection was conducted using the Illumina/Hiseq-2000 RNA-Seq technology. A total of 56,345,139 clean reads were generated and then assembled into 74,007 unigenes with an average length of 680 bp and an N50 of 1197 bp. Unigenes were annotated by comparing against non-redundant protein sequence (nr), non-redundant nucleotide (nt), Swiss-Prot, Pfam, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and 29,615 unigenes (40.01%) were annotated in at least one database. There were 636 genes (518 up-regulated and 118 down-regulated) that were significantly differentially expressed after bacterial challenge, and among which 369 were associated with 122 pathways, including classical immune-related pathways, such as 'MAPK signaling pathway', 'Chemokine signaling pathway', 'Apoptosis' and 'Wnt signaling pathway'. These findings provide information on the pearl oyster innate immunity and may contribute to developing strategies for management of diseases and long-term sustainability of P. fucata culture.

Responses of yeast biocontrol agents to environmental stress

Biological control of postharvest diseases, utilizing wild species and strains of antagonistic yeast species, is a research topic that has received considerable attention in the literature over the past 30 years. In principle, it represents a promising alternative to chemical fungicides for the management of postharvest decay of fruits, vegetables, and grains. A yeast-based biocontrol system is composed of a tritrophic interaction between a host (commodity), a pathogen, and a yeast species, all of which are affected by environmental factors such as temperature, pH, and UV light as well as osmotic and oxidative stresses. Additionally, during the production process, biocontrol agents encounter various severe abiotic stresses that also impact their viability. Therefore, understanding the ecological fitness of the potential yeast biocontrol agents and developing strategies to enhance their stress tolerance are essential to their efficacy and commercial application. The current review provides an overview of the responses of antagonistic yeast species to various environmental stresses, the methods that can be used to improve stress tolerance and efficacy, and the related mechanisms associated with improved stress tolerance.

Evaluation of yeasts from Tibetan fermented products as agents for biocontrol of blue mold of Nashi pear fruits

A total of 20 strains of yeast isolated from Tibetan fermented products were screened for antagonism against blue mold of pear caused by Penicillium expansum. Six isolates that inhibited incidence of postharvest decay by 35% or more were selected for further screening. Among them, the most effective was Rhodotorula mucilaginosa. The results showed that washed cell suspensions of R. mucilaginosa yielded better antagonistic efficacy than unwashed cell-culture mixtures, cell-free culture filtrates, and autoclaved cell cultures. Biocontrol activity improved with increasing concentrations of incubated cells. The best concentration was 1×10(8) cells/ml, at which the incidence of decay was only 16.7% after 6 d of incubation. The germination of conidia of P. expansum in vitro was significantly inhibited by both washed cell-suspensions and unwashed cell-culture mixtures. Rapid colonization by yeast at different concentrations showed a relationship between yeast-cell concentration and biocontrol activity. Although the titratable acidity of pear fruits increased after treatment, R. mucilaginosa did not affect the total soluble solids or ascorbic acid content. This is the first study to report that the yeast R. mucilaginosa from Tibet Autonomous Region of China may have potential as an antagonist to control the postharvest decay of pear fruits.

Biocontrol ability and action mechanism of food-isolated yeast strains against Botrytis cinerea causing post-harvest bunch rot of table grape

Strains belonging to the species Saccharomyces cerevisiae, Wickerhamomyces anomalus, Metschnikowia pulcherrima and Aureobasidium pullulans, isolated from different food sources, were tested in vitro as biocontrol agents (BCAs) against the post-harvest pathogenic mold Botrytis cinerea. All yeast strains demonstrated antifungal activity at different levels depending on species and medium. Killer strains of W. anomalus and S. cerevisiae showed the highest biocontrol in vitro activity, as demonstrated by largest inhibition halos. The competition for iron and the ability to form biofilm and to colonize fruit wounds were hypothesized as the main action mechanisms for M. pulcherrima. The production of hydrolytic enzymes and the ability to colonize the wounds were the most important mechanisms for biocontrol activity in A. pullulans and W. anomalus, which also showed high ability to form biofilm. The production of volatile organic compounds (VOCs) with in vitro and in vivo inhibitory effect on pathogen growth was observed for the species W. anomalus, S. cerevisiae and M. pulcherrima. Our study clearly indicates that multiple modes of action may explain as M. pulcherrima provide excellent control of postharvest botrytis bunch rot of grape.

Mechanisms of action for 2-phenylethanol isolated from Kloeckera apiculata in control of Penicillium molds of citrus fruits

BACKGROUND

Green and blue mold decay, caused by Penicillium digitatum and P. italicum, respectively, are important postharvest diseases of citrus. Biocontrol by microbes is an alternative to synthetic fungicide application. In this study, the antagonistic yeast strain Kloeckera apiculata 34-9 was used to investigate the action mechanisms involved in the biocontrol of postharvest diseases.

RESULTS

An antifungal substance, 2-phenylethanol (PEA), was isolated from K. apiculata and demonstrated to have antimicrobial activity against selected phytopathogenic fungi. Experiments on P. italicum cells identified the mitochondria and the nucleus as particularly sensitive to inhibition. Regulation of P. italicum gene expression was investigated using RNA-Seq. PEA up-regulated genes involved with the peroxisome, regulation of autophagy, phosphatidylinositol signaling system, protein processing in endoplasmic reticulum, fatty acid metabolism, and inhibited ribosome, RNA polymerase, DNA replication, amino acid biosynthesis, aminoacyl-tRNA biosynthesis and cell cycle. Inhibitory responses revealed by RNA-Seq suggest that PEA might compete for attachment on the active site of phenylalanyl-tRNA synthetase (PheRS).

CONCLUSION

This study provided new insight on the mode of action of biocontrol yeast agents in controlling postharvest pathogenic fungi.

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea

BACKGROUND

The olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption.

RESULTS

Transcriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models.

CONCLUSION

Based on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.

De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress

Salinity stress is one of the most serious factors that impede the growth and development of various crops. Wild Gossypium species, which are remarkably tolerant to salt water immersion, are valuable resources for understanding salt tolerance mechanisms of Gossypium and improving salinity resistance in upland cotton. To generate a broad survey of genes with altered expression during various stages of salt stress, a mixed RNA sample was prepared from the roots and leaves of Gossypium aridum plants subjected to salt stress. The transcripts were sequenced using the Illumina sequencing platform. After cleaning and quality checks, approximately 41.5 million clean reads were obtained. Finally, these reads were eventually assembled into 98,989 unigenes with a mean size of 452 bp. All unigenes were compared to known cluster of orthologous groups (COG) sequences to predict and classify the possible functions of these genes, which were classified into at least 25 molecular families. Variations in gene expression were then examined after exposing the plants to 200 mM NaCl for 3, 12, 72 or 144 h. Sequencing depths of approximately six million raw tags were achieved for each of the five stages of salt stress. There were 2634 (1513 up-regulated/1121 down-regulated), 2449 (1586 up-regulated/863 down-regulated), 2271 (946 up-regulated/1325 down-regulated) and 3352 (933 up-regulated/2419 down-regulated) genes that were differentially expressed after exposure to NaCl for 3, 12, 72 and 144 h, respectively. Digital gene expression analysis indicated that pathways involved in "transport", "response to hormone stimulus" and "signaling" play important roles during salt stress, while genes involved in "protein kinase activity" and "transporter activity" undergo major changes in expression during early and later stages of salt stress, respectively.