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I. J. Holb - One of the best experts on this subject based on the ideXlab platform.

  • preliminary study on micro area based spatial distribution of Monilinia fructigena in an organic apple orchard
    Journal of Horticultural Science, 2014
    Co-Authors: I. J. Holb, A Rozsa, F Abonyi
    Abstract:

    In this study, we aimed to report a preliminary study on micro area based spatial distribution of Monilinia fructigena in an organic apple orchard. Results showed that number of symptomatic fruit ranged between 22 and 42 in 2013 and between 25 and 35 in 2014. Number of asymptomatic fruit ranged between 111 and 187 in 2013 and between 119 and 167 in 2014. Disease incidence of fruit ranged between 19.7 and 23.2% in 2013 and between 19.1 and 26.5% in 2014. Disease aggregation index ranged between 0.111 and 0.335 in 2013 and between 123 and 401 in 2014. Three of the four trees showed significant within canopy aggregation of disease for fruit brown rot symptoms in both years. However, the remaining one tree exhibited random patterns during both years. Disease aggregation indicated a disease spread by fruit-to-fruit contact and/or an aggregatedpattern of insect damage.

  • Disease warning models for brown rot fungi of fruit crops
    International Journal of Horticultural Science, 2013
    Co-Authors: I. J. Holb
    Abstract:

    In this review, disease warning models for brown rot fungi, including Monilinia fructigena, M. laxa and M. fructicola, were summarized. Few studies have been made to relate epidemiology and disease warning in brown rot infection caused by M. fructicola and M. laxa in order to predict infections or develop decision support models for fungicide applications during the growing season. More recently a disease warning model and a decision support system were also performed for M. fructigena for organic apple orchards. This review gives an overview on some details of the above disease warning models and decision support system.

  • diurnal patterns in dispersal of Monilinia fructigena conidia in an apple orchard in relation to weather factors
    Agricultural and Forest Meteorology, 2009
    Co-Authors: Finian Bannon, I. J. Holb, Gerrit Gort, Gerard Van Leeuwen, Michael Jeger
    Abstract:

    Abstract The aerial concentration of Monilinia fructigena (causing brown rot in pome fruit) conidia was sampled during 1997 and 1998 in an apple orchard and was related to weather conditions. The highest hourly concentration measured in 1997 was 230 conidia/m 3 , in 1998 concentrations were lower than in 1997 throughout the season. In both years concentrations were highest in the afternoon hours. Generalised linear models, employing a Poisson distribution for the spore counts and a logarithm link function, were used to study the relationships between spore counts and lagged weather variables. In 1997 the best fitting model had variables temperature lagged at 100 h, an east–west component of wind direction, and wind speed; whereas in 1998 the best model included in addition an effect of relative humidity. Temperature and wind direction had consistent effects on hourly spore counts in both years, but whereas temperature has a biologically relevant effect on spore production and maturation, the effect of wind direction is likely to reflect the purely local effect of orchard layout. Results are compared with observations made in stone fruit orchards where Monilinia laxa and Monilinia fructicola are the predominant species, and differences in epidemiology between these systems are discussed.

  • monitoring conidial density of Monilinia fructigena in the air in relation to brown rot development in integrated and organic apple orchards
    European Journal of Plant Pathology, 2008
    Co-Authors: I. J. Holb
    Abstract:

    In a three-year Hungarian study, conidial density of Monilinia fructigena in the air determined from mid-May until harvest was related to brown rot disease progress in integrated and organic apple orchards. Conidia of M. fructigena were first trapped in late May in both orchards in all years. Number of conidial density greatly increased after the appearance of first infected fruit, from early July in the organic and from early August in the integrated orchard. Conidial number continuously increased until harvest in both orchards. Final brown rot incidence reached 4.3–6.6% and 19.8–24.5% in the integrated and organic orchards, respectively. Disease incidence showed a significant relationship with corresponding cumulative numbers of trapped conidia both in integrated and organic orchards, and was described by separate three-parameter Gompertz functions for the two orchards. Time series analyses, using autoregressive integrated moving average (ARIMA) models, revealed that the temporal patterns of the number of airborne conidia was similar in all years in both integrated and organic orchards. Conidia caught over a 24-h period showed distinct diurnal periodicity, with peak spore density occurring in the afternoon between 13.00 and 18.00. Percent viability of M. fructigena conidia ranged from 48.8 to 70.1% with lower viability in dry compared to wet days in both orchards and all years. Temperature and relative humidity correlated best with mean hourly conidial catches in both integrated and organic apple orchards in each year. Correlations between aerial spore density and wind speed were significant only in the organic orchard over the 3-year period. Mean hourly rainfall was negatively but poorly correlated with mean hourly conidial catches. Results were compared and discussed with previous observations.

  • quantitative relationships between different injury factors and development of brown rot caused by Monilinia fructigena in integrated and organic apple orchards
    Phytopathology, 2008
    Co-Authors: I. J. Holb, H Scherm
    Abstract:

    In a 4-year study, the incidence of various types of injuries (caused by insects, birds, growth cracks, mechanical wounding, and other, unidentified factors) was assessed in relation to brown rot development (caused by Monilinia fructigena) on fruit of three apple cultivars (Prima, Jonathan, and Mutsu) in integrated and organic blocks of two apple orchards in Hungary. In addition, populations of male codling moths (Cydia pomonella) were monitored with pheromone traps season-long in both management systems. On average, injury incidence on fruit at harvest was 6.1 and 19.2% in the integrated and organic treatments, respectively. Insect injury, which was caused primarily by C. pomonella, had the highest incidence among the five injury types, accounting for 79.4% of the total injury by harvest in the organic blocks and 36.6% in the integrated blocks. Levels of all other injury types remained close to zero during most of the season, but the incidence of bird injury and growth cracks increased markedly in the final 3 to 5 weeks before harvest in both production systems. Brown rot developed more slowly and reached a lower incidence in the integrated (6.4% final incidence on average) compared with the organic blocks (20.1% average incidence). In addition, the disease developed later but attained higher levels as the cultivar ripening season increased from early-maturing Prima to late-maturing Mutsu. Overall, 94.3 to 98.7% of all injured fruit were also infected by M. fructigena, whereas the incidence of brown-rotted fruit without visible injury was very low (0.8 to 1.6%). Correlation coefficients (on a per plot basis) and association indices (on a per-fruit basis) were calculated between brown rot and the various injury types for two selected assessment dates 4 weeks preharvest and at harvest. At both dates, the strongest significant (P < 0.05) relationships were observed between brown rot and insect injury and between brown rot and the cumulative number of trapped C. pomonella. At the harvest assessment, two additional significant correlations were between brown rot and bird injury and between brown rot and growth cracks. In every case, correlation coefficients were larger in organic than in integrated blocks. Although it is well established that brown rot in pome fruits is closely associated with fruit injuries, this is the first study to provide season-long progress data on different injury types and quantitative analyses of their relative importance at different times in the growing season and across two distinct management systems.

Francesco Faretra - One of the best experts on this subject based on the ideXlab platform.

  • genome sequence of the brown rot fungal pathogen Monilinia fructigena
    BMC Research Notes, 2018
    Co-Authors: Lucia Landi, Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, Francesco Faretra, Gianfranco Romanazzi
    Abstract:

    Monilinia fructigena (phylum Ascomycota, family Sclerotiniaceae) is a plant pathogen that causes brown rot and blossom blight in pome fruit and stone fruit of the Rosaceae family, which can cause significant losses in the field and mainly postharvest. The aim of this study was to create a high-quality draft of the M. fructigena genome assembly and annotation that provides better understanding of the epidemiology of the pathogen and its interactions with the host(s) and will thus improve brown rot management. We report here on the genome sequence of M. fructigena strain Mfrg269 that was collected from plum in southern Italy. This is assembled into 131 scaffolds, with a total size of 43.125 Mb, with 9960 unique protein-coding genes. The novel genomic resources allow improved genomic comparisons among the most important pathogens belonging to the Monilinia genus, with the aim being to improve the knowledge of their plant–pathogen interactions, population biology, and control.

  • de novo assembly and comparative transcriptome analysis of Monilinia fructicola Monilinia laxa and Monilinia fructigena the causal agents of brown rot on stone fruits
    BMC Genomics, 2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, D Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses. Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements. This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.

  • De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits
    BMC Genomics, 2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Background Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola , M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses. Results Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola , 31,103 for M. laxa and 28,890 for M. fructigena . Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea , Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola , 30 in M. laxa and 31 in M. fructigena . Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements. Conclusions This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola , M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.

  • Genome sequence of the brown rot fungal pathogen Monilinia fructigena
    BMC, 2018
    Co-Authors: Lucia Landi, Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, Francesco Faretra, Gianfranco Romanazzi
    Abstract:

    Abstract Objectives Monilinia fructigena (phylum Ascomycota, family Sclerotiniaceae) is a plant pathogen that causes brown rot and blossom blight in pome fruit and stone fruit of the Rosaceae family, which can cause significant losses in the field and mainly postharvest. The aim of this study was to create a high-quality draft of the M. fructigena genome assembly and annotation that provides better understanding of the epidemiology of the pathogen and its interactions with the host(s) and will thus improve brown rot management. Data description We report here on the genome sequence of M. fructigena strain Mfrg269 that was collected from plum in southern Italy. This is assembled into 131 scaffolds, with a total size of 43.125 Mb, with 9960 unique protein-coding genes. The novel genomic resources allow improved genomic comparisons among the most important pathogens belonging to the Monilinia genus, with the aim being to improve the knowledge of their plant–pathogen interactions, population biology, and control

  • Additional file 1: of De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits
    2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Table S1. Summary of sequencing data. Table S2. Numbers of mapping reads on the Monilinia fructicola (MFRC), M. laxa (MLAX) and M. fructigena (MFRG) assembled transcriptomes. (DOCX 51 kb

Michael Jeger - One of the best experts on this subject based on the ideXlab platform.

  • diurnal patterns in dispersal of Monilinia fructigena conidia in an apple orchard in relation to weather factors
    Agricultural and Forest Meteorology, 2009
    Co-Authors: Finian Bannon, I. J. Holb, Gerrit Gort, Gerard Van Leeuwen, Michael Jeger
    Abstract:

    Abstract The aerial concentration of Monilinia fructigena (causing brown rot in pome fruit) conidia was sampled during 1997 and 1998 in an apple orchard and was related to weather conditions. The highest hourly concentration measured in 1997 was 230 conidia/m 3 , in 1998 concentrations were lower than in 1997 throughout the season. In both years concentrations were highest in the afternoon hours. Generalised linear models, employing a Poisson distribution for the spore counts and a logarithm link function, were used to study the relationships between spore counts and lagged weather variables. In 1997 the best fitting model had variables temperature lagged at 100 h, an east–west component of wind direction, and wind speed; whereas in 1998 the best model included in addition an effect of relative humidity. Temperature and wind direction had consistent effects on hourly spore counts in both years, but whereas temperature has a biologically relevant effect on spore production and maturation, the effect of wind direction is likely to reflect the purely local effect of orchard layout. Results are compared with observations made in stone fruit orchards where Monilinia laxa and Monilinia fructicola are the predominant species, and differences in epidemiology between these systems are discussed.

  • factors affecting mummification and sporulation of pome fruit infected by Monilinia fructigena in dutch orchards
    Plant Pathology, 2002
    Co-Authors: G C M Van Leeuwen, I. J. Holb, Michael Jeger
    Abstract:

    A 2-year field experiment (1997–98, 1998–99) was conducted to study mummification and subsequent sporulation in spring of apple (cvs James Grieve, Golden Delicious) and pear (cv. Conference) fruits infected by Monilinia fructigena. Most mummified fruits were found in James Grieve and Conference, whereas in late-infected Golden Delicious, fruits were still soft when examined in April. In the first year, these late-infected fruits had a significantly higher sporulation intensity per sporulating fruit (P = 0·05) compared with Golden Delicious fruits infected 9 and 5 weeks before harvest maturity, which were partly mummified. It was concluded that early- and late-infected fruits contributed to primary inoculum in the next season. In a postinfection regime of 25°C and 65–75% relative humidity under controlled conditions, the number of Conference fruits sporulating decreased rapidly, and after 12 weeks’ incubation sporulation had completely ceased. After 8 weeks’ incubation, sporulation intensity in the postinfection regime at 10°C was significantly higher than that at 20 and 25°C in a first experiment with inoculated unripe fruit (P = 0·05). Results of a second experiment with ripe fruit were less clear. These results are discussed in relation to orchard disease management.

  • distinction of the asiatic brown rot fungus monilia polystroma sp nov from m fructigena
    Fungal Biology, 2002
    Co-Authors: Gerard Van Leeuwen, I. J. Holb, R P Baayen, Michael Jeger
    Abstract:

    Monilinia fructigena isolates from Japan were compared with isolates from Europe. General colony characteristics, stroma formation, growth rate and conidial dimensions were determined for six isolates each from both groups, as well as sporulation intensity on potato dextrose agar (PDA) and germ tube features. Potential differences in pathogenicity were tested on the pear cultivars ‘Conference’ and ‘Doyenne du Comice’, and on the apple cultivar ‘Cox's Orange Pippin’. A marked difference in stroma formation occurred, the area of stromatal plates ranged from 4.1 to 5.2 cm 2 in the Japanese group, and from 0 to 0.9 cm 2 in the European. The mean growth rate was significantly higher for Japanese isolates ( t -test, P = 0.01). Length and width of conidia were significantly greater in European isolates ( t -test, P = 0.01). Conidia measured on average 19 x 11.5 μm in European isolates, and 16 x 10 μm in Japanese ones when grown on cherry agar. On fruits, the difference in conidium size was even more pronounced. Sporulation intensity on PDA and germ tube features did not differ between both groups. No differences were found in latency period, lesion growth rate or sporulation intensity on apple and pear fruits between both groups. Together with previously published differences in the ITS region of ribosomal DNA, our results show that the Japanese isolates belong to a distinct species, Monilia polystroma sp. nov. A description of the anamorph is given, as well as a table summarising key features for all four brown rot associated Monilia species.

  • yield loss in apple caused by Monilinia fructigena aderh ruhl honey and spatio temporal dynamics of disease development
    European Journal of Plant Pathology, 2000
    Co-Authors: G C M Van Leeuwen, I. J. Holb, Alfred Stein, Michael Jeger
    Abstract:

    Monilinia fructigena (Aderh. & Ruhl.) Honey causes considerable yield losses in pome fruit culture. During a field study in the Netherlands in 1997 and 1998, the increase in disease incidence in time was assessed and final pre- and post-harvest losses were recorded in the susceptible apple cultivars James Grieve and Cox's Orange Pippin. Each individual tree was considered as a unique quadrat, and the spatial distribution of diseased fruits among fruit trees at every assessment date was characterised by a dispersion index, Lloyd's index of patchiness (LIP). Spatial autocorrelation was applied to detect potential clustering of trees with diseased fruits within rows. In cv. James Grieve, the rate of increase of disease incidence was constant up to harvest time, whereas in cv. Cox's Orange Pippin disease incidence increased markedly 3 weeks before harvest time, which coincided with the harvest of cv. James Grieve in neighbouring rows. Pre-harvest disease incidence was 4.2–4.3% in cv. James Grieve in both years, in cv. Cox's Orange Pippin this was 4.4% in 1997 and 2.7% in 1998. Post-harvest yield losses amounted on average 1.5–2.0% for both cultivars, no significant differences were found between the cultivars (t-test, P=0.05). Both in 1997 and 1998, clustering of diseased fruits among fruit trees was detected; LIP values were significantly higher than 1 (P=0.05 in 1997, P=0.01 in 1998). Clustering of trees with diseased fruits was detected in 1998, when significant (P=0.05) positive correlation coefficients occurred for 2nd, 3rd and 4th lag-order distances in cv. James Grieve, and a significant (P=0.05) positive first-order correlation in cv. Cox's Orange Pippin. Wounding agents, such as insects and birds, may play an important role in the underlying disease dynamics, and crop losses may be minimised by control of these agents.

Gabriella Cirvilleri - One of the best experts on this subject based on the ideXlab platform.

  • postharvest biocontrol ability of pseudomonas synxantha against Monilinia fructicola and Monilinia fructigena on stone fruit
    Postharvest Biology and Technology, 2019
    Co-Authors: D Aiello, Cristina Restuccia, Emilio Stefani, A Vitale, Gabriella Cirvilleri
    Abstract:

    Abstract The biocontrol properties of the endophyte Pseudomonas synxantha DLS65 were tested in vitro and in vivo against Monilinia fructicola and Monilinia fructigena, causal agents of postharvest brown rot of stone fruit. P. synxantha cells significantly reduced the mycelial growth of both pathogens on Potato Dextrose Agar (PDA), and strongly inhibited the Monilinia fructicola growth on Peach Extract Agar (PEA). Cell-free culture filtrates inhibited the pathogens on PDA and PEA to lesser extent. The production of volatile organic compounds (VOCs), with in vitro inhibitory effects on mycelial growth, was also observed. P. synxantha significantly reduced brown rot incidence and severity on peach fruit artificially inoculated with M. fructicola after 5 d at 25 °C. Moreover, P. synxantha more significantly reduced incidence and severity after 10 d at 10 °C and after 20 d in cold storage at 0 °C in comparison to control fruit, even if its activity was never comparable to that of the synthetic fungicide Scholar® (fludioxonil). Similarly, P. synxantha exhibited an excellent antagonistic activity against M. fructigena on fruit at 10 and at 0 °C, and a weak biocontrol activity at 25 °C. Competition for nutrients and space, production of diffusible toxic metabolites and VOCs may play a role in the antagonism of P. synxantha toward M. fructicola and M. fructigena, especially at the lowest temperatures of storage. For that reason, this strain of P. synxantha could be suggested as active ingredient for the setting up of bioformulates against Monilinia species representing a limiting factor for stone fruit production.

  • postharvest biocontrol ability of killer yeasts against Monilinia fructigena and Monilinia fructicola on stone fruit
    Food Microbiology, 2017
    Co-Authors: Monika Grzegorczyk, Barbara żarowska, Cristina Restuccia, Gabriella Cirvilleri
    Abstract:

    Abstract The antagonistic effects of Debaryomyces hansenii KI2a, D. hansenii MI1a and Wickerhamomyces anomalus BS91 were tested against Monilinia fructigena and Monilinia fructicola in in vitro and in vivo trials. All yeast strains demonstrated antifungal activity at different levels depending on species, strain and pathogen. D hansenii KI2a and W. anomalus BS91 showed the highest biocontrol activity in vitro ; the production of hydrolytic enzymes, killer toxins and volatile organic compounds (VOCs) were hypothesized as their main mechanisms of action against pathogens. D hansenii KI2a and W. anomalus BS91 significantly reduced brown rot incidence and severity on peach and plum fruits artificially inoculated with M. fructigena and M. fructicola , especially when applied 24 h before pathogen inoculation. On the opposite, D. hansenii MI1a exhibited weak antagonistic activity towards M. fructigena on peach and plum fruits and was ineffective against M. fructicola . The noticeable ability of W. anomalus BS91 to control brown rot could be also correlated with its high capacity to colonize the wound tissue and to increase its population density. Accordingly, the antagonistic strains of D. hansenii and W. anomalus could be proposed as active ingredients for the development of biofungicides against Monilinia species that are responsible for considerable economic losses in stone fruit crops.

Rita M. De Miccolis Angelini - One of the best experts on this subject based on the ideXlab platform.

  • genome sequence of the brown rot fungal pathogen Monilinia fructigena
    BMC Research Notes, 2018
    Co-Authors: Lucia Landi, Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, Francesco Faretra, Gianfranco Romanazzi
    Abstract:

    Monilinia fructigena (phylum Ascomycota, family Sclerotiniaceae) is a plant pathogen that causes brown rot and blossom blight in pome fruit and stone fruit of the Rosaceae family, which can cause significant losses in the field and mainly postharvest. The aim of this study was to create a high-quality draft of the M. fructigena genome assembly and annotation that provides better understanding of the epidemiology of the pathogen and its interactions with the host(s) and will thus improve brown rot management. We report here on the genome sequence of M. fructigena strain Mfrg269 that was collected from plum in southern Italy. This is assembled into 131 scaffolds, with a total size of 43.125 Mb, with 9960 unique protein-coding genes. The novel genomic resources allow improved genomic comparisons among the most important pathogens belonging to the Monilinia genus, with the aim being to improve the knowledge of their plant–pathogen interactions, population biology, and control.

  • de novo assembly and comparative transcriptome analysis of Monilinia fructicola Monilinia laxa and Monilinia fructigena the causal agents of brown rot on stone fruits
    BMC Genomics, 2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, D Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses. Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements. This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.

  • De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits
    BMC Genomics, 2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Background Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola , M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses. Results Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola , 31,103 for M. laxa and 28,890 for M. fructigena . Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea , Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola , 30 in M. laxa and 31 in M. fructigena . Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements. Conclusions This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola , M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.

  • Genome sequence of the brown rot fungal pathogen Monilinia fructigena
    BMC, 2018
    Co-Authors: Lucia Landi, Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, Francesco Faretra, Gianfranco Romanazzi
    Abstract:

    Abstract Objectives Monilinia fructigena (phylum Ascomycota, family Sclerotiniaceae) is a plant pathogen that causes brown rot and blossom blight in pome fruit and stone fruit of the Rosaceae family, which can cause significant losses in the field and mainly postharvest. The aim of this study was to create a high-quality draft of the M. fructigena genome assembly and annotation that provides better understanding of the epidemiology of the pathogen and its interactions with the host(s) and will thus improve brown rot management. Data description We report here on the genome sequence of M. fructigena strain Mfrg269 that was collected from plum in southern Italy. This is assembled into 131 scaffolds, with a total size of 43.125 Mb, with 9960 unique protein-coding genes. The novel genomic resources allow improved genomic comparisons among the most important pathogens belonging to the Monilinia genus, with the aim being to improve the knowledge of their plant–pathogen interactions, population biology, and control

  • Additional file 1: of De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits
    2018
    Co-Authors: Rita M. De Miccolis Angelini, Stefania Pollastro, Domenico Abate, C Rotolo, D Gerin, Francesco Faretra
    Abstract:

    Table S1. Summary of sequencing data. Table S2. Numbers of mapping reads on the Monilinia fructicola (MFRC), M. laxa (MLAX) and M. fructigena (MFRG) assembled transcriptomes. (DOCX 51 kb