Plants must adapt with increasing speed to global warming to maintain their fitness.One rapid adaptation mechanism is epigenetic memory,which may provide organisms sufficient time to adapt to climate change.We studied...Plants must adapt with increasing speed to global warming to maintain their fitness.One rapid adaptation mechanism is epigenetic memory,which may provide organisms sufficient time to adapt to climate change.We studied how the perennial Fragaria vesca adapted to warmer temperatures(28◦C vs.18◦C)over three asexual generations.Differences in flowering time,stolon number,and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment.Induced methylome changes differed between the four ecotypes from Norway,Iceland,Italy,and Spain,but shared methylome responses were also identified.Most differentially methylated regions(DMRs)occurred in the CHG context,and most CHG and CHH DMRs were hypermethylated at the warmer temperature.In eight CHG DMR peaks,a highly similar methylation pattern could be observed between ecotypes.On average,13%of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression.We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism,flowering time,and epigenetic mechanisms.Furthermore,we observed a negative correlation with gene expression when repetitive elements were found near(±2 kb)or inside genes.In conclusion,lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns.Both shared methylation patterns and transcriptome differences between F.vesca accessions were observed,indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.展开更多
The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved i...The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.展开更多
Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original a...Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original article has been corrected.展开更多
文摘Plants must adapt with increasing speed to global warming to maintain their fitness.One rapid adaptation mechanism is epigenetic memory,which may provide organisms sufficient time to adapt to climate change.We studied how the perennial Fragaria vesca adapted to warmer temperatures(28◦C vs.18◦C)over three asexual generations.Differences in flowering time,stolon number,and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment.Induced methylome changes differed between the four ecotypes from Norway,Iceland,Italy,and Spain,but shared methylome responses were also identified.Most differentially methylated regions(DMRs)occurred in the CHG context,and most CHG and CHH DMRs were hypermethylated at the warmer temperature.In eight CHG DMR peaks,a highly similar methylation pattern could be observed between ecotypes.On average,13%of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression.We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism,flowering time,and epigenetic mechanisms.Furthermore,we observed a negative correlation with gene expression when repetitive elements were found near(±2 kb)or inside genes.In conclusion,lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns.Both shared methylation patterns and transcriptome differences between F.vesca accessions were observed,indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.
基金Estonian Science Foundation grants PSG136,PRG632,PUT1170the University of Tartu(PLTOM20903)the European Regional Development Fund(Centre of Excellence EcolChange).
文摘The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.
文摘Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original article has been corrected.