Uncultured fungus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA549005 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spanish fir (Abies pinsapo) is a relict tree that is found in southern Spain mountains. In natural conditions two phenotypes can be observed, trees with blue needles and trees with green needles. The aim of the present work is to elucidate at transcriptomic levels the possible causes of the differences between these phenotypes.
2021-11-20 | GSE189122 | GEO
Project description:Endomycobiotas of the last four cohorts of Abies balsamea needles display relatively similar diversities but different compositions
| PRJNA549007 | ENA
Project description:Differences in endophyte communities of introduced trees depend on the phylogenetic relatedness of the receiving forest
| PRJNA317929 | ENA
Project description:Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.
2016-09-20 | GSE73420 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE10058: Microarray assay of the genetic response of Picea abies to Heterobasidion annosum infection - Loop1 GSE10059: Microarray assay of the genetic response of Picea abies to Heterobasidion annosum infection - Loop2 The hypothesis of the experiment is that infected trees of high resistance express a wider variety of resistance genes than infected trees of low resistance, and that the level of expression of these resistance genes differs between infected and healthy branches. Also, some genes highly expressed in the infected state not expressed in the healthy state may be in response to the wounding rather than the actual infection. By comparing these expressions to that of wounded, uninfected branches, this could also be clarified. Refer to individual Series
2008-05-03 | E-GEOD-11323 | biostudies-arrayexpress
Project description:The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 "uncultured fungus" sequences that represent truly unidentifiable fungal taxa - and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
| S-EPMC8828591 | biostudies-literature
Project description:The conservation of the endangered Korean fir, Abies koreana, is of critical ecological importance. In our previous study, a yeast-like fungus identified as Aureobasidium pullulans AK10, was isolated and shown to enhance drought tolerance in A. koreana seedlings. In this study, the effectiveness of A. pullulans AK10 treatment in enhancing drought tolerance in A. koreana was confirmed. Furthermore, using transcriptome analysis, we compared A. koreana seedlings treated with A. pullulans AK10 to untreated controls under drought conditions to elucidate the molecular responses involved in increased drought tolerance.
2024-02-14 | GSE248350 | GEO