Papers by Letterio Giuffrè
The isolation of patulin-producing Penicillia in apples collected in different markets in four lo... more The isolation of patulin-producing Penicillia in apples collected in different markets in four localities inMorocco is reported. Fungi were identified by β-tubulin sequencing and further characterized using a specific PCR-based method targeting the isoepoxydon dehydrogenase (IDH) gene to discriminate between patulin-producing and non-producing strains. Production of patulin was also evaluated using standard cultural and biochemical methods.
Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%).
Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin productionwas not chemically confirmed in all P. expansum strains.
The isolation of IDH−/patulin+ strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of
P. expansum strains and for 100% of the other species isolated.
Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco.
Background
In this study we report the genetic characterization, including expression analysis, o... more Background
In this study we report the genetic characterization, including expression analysis, of the
genes involved in the uptake (NGT1) and catabolism (HXK1/NAG5, DAC1/NAG2, NAG1) of
the aminosugar N-acetylglucosamine (GlcNAc) in Candida africana, a pathogenic biovar-
iant of Candida albicans that is naturally unable to assimilate the GlcNAc.
Results
DNA sequence analysis of these genes revealed a number of characteristic nucleotide sub-
stitutions including a unique and distinctive guanine insertion that shifts the reading frame
and generates a premature stop codon (TGA) 154 bp downstream of the ATG start codon
of the HXK1 gene encoding the GlcNAc-kinase, a key enzyme of the GlcNAc catabolic path-
way. However, all examined genes produced transcripts even though different levels of
expression were observed among the Candida isolates examined. In particular, we found
an HXK1-idependent relationship of the NGT1 gene and a considerable influence of the
GlcNAc-kinase functionality on the transcription of the DAC1 and NAG1 genes. Additional
phenotypic analysis revealed that C. africana isolates are hyperfilamentous in the first 24-
48h of growth on filament-inducing media and revert to the yeast morphological form after
72h of incubation on these media.
Conclusions
Our results show that C. africana is a natural HXK1 mutant, displaying a number of pheno-
typic characteristics distinct from typical C. albicans isolates.
Conference Presentations by Letterio Giuffrè
Candida albicans is the most common opportunistic pathogen causing severe fungal infection in hum... more Candida albicans is the most common opportunistic pathogen causing severe fungal infection in humans, especially in immunocompromised patients. Crucial to its success as a pathogen is the substantial dynamism of its genome which readily undergoes genetic changes generating new strains. Candida africana is a low virulence biovariant of C. albicans possessing peculiar vaginal tropism. This particular strain is
unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.
Goats (Capra hircus) are spread worldwide following human migrations and commercial trade and are... more Goats (Capra hircus) are spread worldwide following human migrations and commercial trade and are rapidly adapted to a very wide range of environmental conditions. Because of their important role in the production of milk, meat and fiber (e.g., cashmere wool), the genetic diversity of many goat populations is changing. Secondary characters, like shape of the horns and coat color, are commonly used to discriminate among breeds, and two genes (KIT and RXFP2) are well known to be involved in these phenotypes.
Here we present SNPs discovery using massively parallel sequencing approach, comparing 6 breeds.
Blood samples from 36 goats (Derivata di Siria, Maltese, Girgentana, Camosciata delle Alpi, Argentata dell’Etna, Saanen) were used to extract genomic DNA for library preparation and sequencing with the Ion Torrent PGM machine. Generated 1,242,457 raw reads were analyzed using Torrent Suite (v.4.2.1), with modules TMAP for the mapping on the reference sequences (Accession: NC_030813, NC_030819) and TVC for the SNPs variant calling.
A total number of 284 variants (~93 each breed) were obtained, 16 of which were shared between all breeds; of these, one was found in heterozygosity with a second alternative variant only in Derivata di Siria and Girgentana. Remaining 258 unshared SNPs (90,84%) highlight the large variability between these breeds.
Our results confirmed the high genetic variability in goat’s population that represent a crucial point to monitor genetic erosion and to evaluate the conservation of the Italian’s goat breeds.
In recent years, there has been a growing interest in the study of the basic biology and genetics... more In recent years, there has been a growing interest in the study of the basic biology and genetics of toxigenic
Penicillia because of their natural occurrence in food products and of the toxic effects of their secondary
metabolites on humans.
Among Penicillium species, Penicillium expansum is a well-known postharvest pathogen causing decay of
apple fruits during storage and it is also responsible for patulin biosynthesis, a mycotoxin that exhibits a
number of toxic effects in mammals.
In this study, authors report the isolation of patulin-producing Penicillia in apples collected in different
markets in four localities in Morocco.
Sequencing data showed that 79.5% of contaminant fungi belonged to Penicillium genus and P. expansum
was the most isolated species followed by P. chrysogenum (~9.7%), P. crustosum (~6.4%) and P. polonicum
(~3.3%).
Molecular analysis revealed that 67.5% of the Penicillium species produced the expected IDH-amplicon
denoting patulin production in these strains. However, patulin production was not chemically confirmed
in all P. expansum and the isolation of IDH-/patulin+ strains poses the hypothesis that the gentisylaldehyde
is not a direct patulin precursor supporting previous observations that highlighted the importance of the
gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and chemical method employed was observed in 54.8% of
the P. expansum and for 100% of the other species.
Overall the data reported here showed considerable epidemiological differences and a substantial genetic
variability within P. expansum population from Morocco.
Th is research was supported in part by the EU Mare Nostrum (EUMN-III Call) program of the European
Union, grant agreement n° 2011-4050/001-EMA2. Dr. Sanae Rharmitt was the recipient of a scholarship
signed within the EUMN program (F.S. 1.04.11.01UORI) under supervision of Prof. Orazio Romeo.
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Papers by Letterio Giuffrè
Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%).
Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin productionwas not chemically confirmed in all P. expansum strains.
The isolation of IDH−/patulin+ strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of
P. expansum strains and for 100% of the other species isolated.
Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco.
In this study we report the genetic characterization, including expression analysis, of the
genes involved in the uptake (NGT1) and catabolism (HXK1/NAG5, DAC1/NAG2, NAG1) of
the aminosugar N-acetylglucosamine (GlcNAc) in Candida africana, a pathogenic biovar-
iant of Candida albicans that is naturally unable to assimilate the GlcNAc.
Results
DNA sequence analysis of these genes revealed a number of characteristic nucleotide sub-
stitutions including a unique and distinctive guanine insertion that shifts the reading frame
and generates a premature stop codon (TGA) 154 bp downstream of the ATG start codon
of the HXK1 gene encoding the GlcNAc-kinase, a key enzyme of the GlcNAc catabolic path-
way. However, all examined genes produced transcripts even though different levels of
expression were observed among the Candida isolates examined. In particular, we found
an HXK1-idependent relationship of the NGT1 gene and a considerable influence of the
GlcNAc-kinase functionality on the transcription of the DAC1 and NAG1 genes. Additional
phenotypic analysis revealed that C. africana isolates are hyperfilamentous in the first 24-
48h of growth on filament-inducing media and revert to the yeast morphological form after
72h of incubation on these media.
Conclusions
Our results show that C. africana is a natural HXK1 mutant, displaying a number of pheno-
typic characteristics distinct from typical C. albicans isolates.
Conference Presentations by Letterio Giuffrè
unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.
Here we present SNPs discovery using massively parallel sequencing approach, comparing 6 breeds.
Blood samples from 36 goats (Derivata di Siria, Maltese, Girgentana, Camosciata delle Alpi, Argentata dell’Etna, Saanen) were used to extract genomic DNA for library preparation and sequencing with the Ion Torrent PGM machine. Generated 1,242,457 raw reads were analyzed using Torrent Suite (v.4.2.1), with modules TMAP for the mapping on the reference sequences (Accession: NC_030813, NC_030819) and TVC for the SNPs variant calling.
A total number of 284 variants (~93 each breed) were obtained, 16 of which were shared between all breeds; of these, one was found in heterozygosity with a second alternative variant only in Derivata di Siria and Girgentana. Remaining 258 unshared SNPs (90,84%) highlight the large variability between these breeds.
Our results confirmed the high genetic variability in goat’s population that represent a crucial point to monitor genetic erosion and to evaluate the conservation of the Italian’s goat breeds.
Penicillia because of their natural occurrence in food products and of the toxic effects of their secondary
metabolites on humans.
Among Penicillium species, Penicillium expansum is a well-known postharvest pathogen causing decay of
apple fruits during storage and it is also responsible for patulin biosynthesis, a mycotoxin that exhibits a
number of toxic effects in mammals.
In this study, authors report the isolation of patulin-producing Penicillia in apples collected in different
markets in four localities in Morocco.
Sequencing data showed that 79.5% of contaminant fungi belonged to Penicillium genus and P. expansum
was the most isolated species followed by P. chrysogenum (~9.7%), P. crustosum (~6.4%) and P. polonicum
(~3.3%).
Molecular analysis revealed that 67.5% of the Penicillium species produced the expected IDH-amplicon
denoting patulin production in these strains. However, patulin production was not chemically confirmed
in all P. expansum and the isolation of IDH-/patulin+ strains poses the hypothesis that the gentisylaldehyde
is not a direct patulin precursor supporting previous observations that highlighted the importance of the
gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and chemical method employed was observed in 54.8% of
the P. expansum and for 100% of the other species.
Overall the data reported here showed considerable epidemiological differences and a substantial genetic
variability within P. expansum population from Morocco.
Th is research was supported in part by the EU Mare Nostrum (EUMN-III Call) program of the European
Union, grant agreement n° 2011-4050/001-EMA2. Dr. Sanae Rharmitt was the recipient of a scholarship
signed within the EUMN program (F.S. 1.04.11.01UORI) under supervision of Prof. Orazio Romeo.
Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%).
Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin productionwas not chemically confirmed in all P. expansum strains.
The isolation of IDH−/patulin+ strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of
P. expansum strains and for 100% of the other species isolated.
Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco.
In this study we report the genetic characterization, including expression analysis, of the
genes involved in the uptake (NGT1) and catabolism (HXK1/NAG5, DAC1/NAG2, NAG1) of
the aminosugar N-acetylglucosamine (GlcNAc) in Candida africana, a pathogenic biovar-
iant of Candida albicans that is naturally unable to assimilate the GlcNAc.
Results
DNA sequence analysis of these genes revealed a number of characteristic nucleotide sub-
stitutions including a unique and distinctive guanine insertion that shifts the reading frame
and generates a premature stop codon (TGA) 154 bp downstream of the ATG start codon
of the HXK1 gene encoding the GlcNAc-kinase, a key enzyme of the GlcNAc catabolic path-
way. However, all examined genes produced transcripts even though different levels of
expression were observed among the Candida isolates examined. In particular, we found
an HXK1-idependent relationship of the NGT1 gene and a considerable influence of the
GlcNAc-kinase functionality on the transcription of the DAC1 and NAG1 genes. Additional
phenotypic analysis revealed that C. africana isolates are hyperfilamentous in the first 24-
48h of growth on filament-inducing media and revert to the yeast morphological form after
72h of incubation on these media.
Conclusions
Our results show that C. africana is a natural HXK1 mutant, displaying a number of pheno-
typic characteristics distinct from typical C. albicans isolates.
unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.
Here we present SNPs discovery using massively parallel sequencing approach, comparing 6 breeds.
Blood samples from 36 goats (Derivata di Siria, Maltese, Girgentana, Camosciata delle Alpi, Argentata dell’Etna, Saanen) were used to extract genomic DNA for library preparation and sequencing with the Ion Torrent PGM machine. Generated 1,242,457 raw reads were analyzed using Torrent Suite (v.4.2.1), with modules TMAP for the mapping on the reference sequences (Accession: NC_030813, NC_030819) and TVC for the SNPs variant calling.
A total number of 284 variants (~93 each breed) were obtained, 16 of which were shared between all breeds; of these, one was found in heterozygosity with a second alternative variant only in Derivata di Siria and Girgentana. Remaining 258 unshared SNPs (90,84%) highlight the large variability between these breeds.
Our results confirmed the high genetic variability in goat’s population that represent a crucial point to monitor genetic erosion and to evaluate the conservation of the Italian’s goat breeds.
Penicillia because of their natural occurrence in food products and of the toxic effects of their secondary
metabolites on humans.
Among Penicillium species, Penicillium expansum is a well-known postharvest pathogen causing decay of
apple fruits during storage and it is also responsible for patulin biosynthesis, a mycotoxin that exhibits a
number of toxic effects in mammals.
In this study, authors report the isolation of patulin-producing Penicillia in apples collected in different
markets in four localities in Morocco.
Sequencing data showed that 79.5% of contaminant fungi belonged to Penicillium genus and P. expansum
was the most isolated species followed by P. chrysogenum (~9.7%), P. crustosum (~6.4%) and P. polonicum
(~3.3%).
Molecular analysis revealed that 67.5% of the Penicillium species produced the expected IDH-amplicon
denoting patulin production in these strains. However, patulin production was not chemically confirmed
in all P. expansum and the isolation of IDH-/patulin+ strains poses the hypothesis that the gentisylaldehyde
is not a direct patulin precursor supporting previous observations that highlighted the importance of the
gentisyl alcohol in the production of this mycotoxin.
Total agreement between IDH-gene detection and chemical method employed was observed in 54.8% of
the P. expansum and for 100% of the other species.
Overall the data reported here showed considerable epidemiological differences and a substantial genetic
variability within P. expansum population from Morocco.
Th is research was supported in part by the EU Mare Nostrum (EUMN-III Call) program of the European
Union, grant agreement n° 2011-4050/001-EMA2. Dr. Sanae Rharmitt was the recipient of a scholarship
signed within the EUMN program (F.S. 1.04.11.01UORI) under supervision of Prof. Orazio Romeo.