To decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv.‘Abate Fetel’,a RNA-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages.These ...To decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv.‘Abate Fetel’,a RNA-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages.These genes were grouped into 11 SOTA clusters based on their transcriptional pattern,of which three included genes upregulated while the other four were represented by downregulated genes.Fruit ripening was furthermore investigated after 1 month of postharvest cold storage.The most important variation in fruit firmness,production of ethylene and volatile organic compounds were observed after 5 days of shelf-life at room temperature following cold storage.The role of ethylene in controlling the ripening of‘Abate Fetel’pears was furthermore investigated through the application of 1-methylcyclopropene,which efficiently delayed the progression of ripening by reducing fruit softening and repressing both ethylene and volatile production.The physiological response of the interference at the ethylene receptor level was moreover unraveled investigating the expression pattern of 12 candidate genes,initially selected to validate the RNA-seq profile.This analysis confirmed the effective role of the ethylene competitor in downregulating the expression of cell wall(PG)and ethylene-related genes(ACS,ACO,ERS1,and ERS2),as well as inducing one element involved in the auxin signaling pathway(Aux/IAA),highlighting a possible cross-talk between these two hormones.The expression patterns of these six elements suggest their use as molecular toolkit to monitor at molecular level the progression of the fruit on-tree maturation and postharvest ripening.展开更多
Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions.The terroir,namely the set of agri-environmental factors to which a variety is subjected,can influenc...Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions.The terroir,namely the set of agri-environmental factors to which a variety is subjected,can influence the phenotype at the physiological,molecular,and biochemical level,representing an important phenomenon connected to the typicality of productions.We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables,except soil,were kept as constant as possible.We isolated the effect of soils collected from different areas,on phenology,physiology,and transcriptional responses of skin and flesh of a red and a white variety of great economic value:Corvina and Glera.Molecular results,together with physio-phenological parameters,suggest a specific effect of soil on grapevine plastic response,highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh.Using a novel statistical approach,we identified clusters of plastic genes subjected to the specific influence of soil.These findings could represent an issue of applicative value,posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination,to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect.展开更多
The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide.Yet,despite the growing interes...The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide.Yet,despite the growing interest in these fungi,there is a considerable gap of knowledge on their functionality.Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited.Here,we supply a genome catalog of 118 black fungi,encompassing different ecologies,phylogenies and lifestyles,as a first example of a comparative genomic study at high level of diversity.Results indicate that,as a rule,Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions;low temperature tolerance and DNA repair capacity are overrepresented in their genomes.In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence.The genomic features are consistent with the prevalent ecologies in the two classes.Indeed,Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats;in contrast,Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution.Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes,suggesting that,despite their preference for the cold,they are potentially equipped to survive even when temperatures rise due to the global warming.展开更多
基金supported by AgroFresh and the National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383.URL:www.cyverse.org.
文摘To decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv.‘Abate Fetel’,a RNA-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages.These genes were grouped into 11 SOTA clusters based on their transcriptional pattern,of which three included genes upregulated while the other four were represented by downregulated genes.Fruit ripening was furthermore investigated after 1 month of postharvest cold storage.The most important variation in fruit firmness,production of ethylene and volatile organic compounds were observed after 5 days of shelf-life at room temperature following cold storage.The role of ethylene in controlling the ripening of‘Abate Fetel’pears was furthermore investigated through the application of 1-methylcyclopropene,which efficiently delayed the progression of ripening by reducing fruit softening and repressing both ethylene and volatile production.The physiological response of the interference at the ethylene receptor level was moreover unraveled investigating the expression pattern of 12 candidate genes,initially selected to validate the RNA-seq profile.This analysis confirmed the effective role of the ethylene competitor in downregulating the expression of cell wall(PG)and ethylene-related genes(ACS,ACO,ERS1,and ERS2),as well as inducing one element involved in the auxin signaling pathway(Aux/IAA),highlighting a possible cross-talk between these two hormones.The expression patterns of these six elements suggest their use as molecular toolkit to monitor at molecular level the progression of the fruit on-tree maturation and postharvest ripening.
基金The study was carried out within the Agritech National Research Center and received funding from the European Union Next-Generation EU(PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR)-MISSIONE 4 COMPONENTE 2,INVESTIMENTO 1.4-D.D.103217/06/2022,CN00000022).
文摘Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions.The terroir,namely the set of agri-environmental factors to which a variety is subjected,can influence the phenotype at the physiological,molecular,and biochemical level,representing an important phenomenon connected to the typicality of productions.We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables,except soil,were kept as constant as possible.We isolated the effect of soils collected from different areas,on phenology,physiology,and transcriptional responses of skin and flesh of a red and a white variety of great economic value:Corvina and Glera.Molecular results,together with physio-phenological parameters,suggest a specific effect of soil on grapevine plastic response,highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh.Using a novel statistical approach,we identified clusters of plastic genes subjected to the specific influence of soil.These findings could represent an issue of applicative value,posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination,to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect.
基金supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No.702057(DRYLIFE)M.D-B.is supported by a project from the Spanish Ministry of Science and Innovation(PID2020-115813RA-I00)+4 种基金a project of the Fondo Europeo de Desarrollo Regional(FEDER)the Consejería de Transformación Económica,Industria,Conocimiento y Universidades of the Junta de Andalucía(FEDER Andalucía 2014-2020 Objetivo temático'01-Refuerzo de la investigación,el desarrollo tecnológico y la innovación')associated with the research project P20_00879(ANDABIOMA)N.S.receives funding from the ERC(ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015)J.E.S.is a CIFAR fellow in the Fungal Kingdom:Threats and Opportunities program.T.K.and J.E.S.were partially supported by NIH NIAID R01-GM108492Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290.
文摘The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide.Yet,despite the growing interest in these fungi,there is a considerable gap of knowledge on their functionality.Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited.Here,we supply a genome catalog of 118 black fungi,encompassing different ecologies,phylogenies and lifestyles,as a first example of a comparative genomic study at high level of diversity.Results indicate that,as a rule,Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions;low temperature tolerance and DNA repair capacity are overrepresented in their genomes.In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence.The genomic features are consistent with the prevalent ecologies in the two classes.Indeed,Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats;in contrast,Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution.Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes,suggesting that,despite their preference for the cold,they are potentially equipped to survive even when temperatures rise due to the global warming.
