Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1186394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31360600_1.fastq.gz | Fastqsanger.gz | |||
| SRR31360600_2.fastq.gz | Fastqsanger.gz | |||
| SRR31360601_1.fastq.gz | Fastqsanger.gz | |||
| SRR31360601_2.fastq.gz | Fastqsanger.gz | |||
| SRR31360602_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.
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Project description:Climate change forecasts increase the susceptibility of forest due to longer drier seasons. The adaptive management protocols have highlighted the reduction of the forest densification to improve their vulnerability to extreme climate events (i.g. drought). One of this sensitive woody species to climate change is the Abies pinsapo, a relic conifer tree endemic from the southern Spain. Previous works have shown changes in their trends because of the climate change action, being carried out experimental thinning management in their lowest distribution limit, in Sierra de las Nieves Natural Park (Malaga). Our objective is to evaluate the water improvements of thinned trees in terms of light availability by means of a shading treatment in those thinned trees. To do that we have evaluated the synergic effect of ecophysiology, metabolomics and transcriptomics in control, thinning and thinning+shading plots in wet and dry seasons for two years. The results showed strong differences between summer and spring seasons at the three studied levels. The water deficit shows a greater influence than light exposure in the ecophysiology and metabolomics tree response. And the transcriptomics suggested an improvement of thinned trees when light exposure was reduced. Our results support the necessity of adaptive forest management in order to improve the conservation status of A. pinsapo forest. The combination of different levels of tree response is paramount to understand and predict the tree physiology under water and light stress conditions.
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Project description:Relationship between the decomposition process of coarse woody debris and fungal community structure as detected by high-throughput sequencing in a deciduous broad-leaved forest in Japan
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Project description:Deadwood plays a crucial role in forest ecosystems, but we have limited information about the specific fungal taxa and extracellular lignocellulolytic enzymes that are actively involved in the decomposition process in situ. To investigate this, we studied the fungal metaproteome of twelve deadwood tree species in a replicated, eight-year experiment. Key fungi observed included genera of white-rot fungi (Basidiomycota, e.g. Armillaria, Hypholoma, Mycena, Ischnoderma, Resinicium), brown-rot fungi (Basidiomycota, e.g. Fomitopsis, Antrodia), diverse Ascomycota including xylariacous soft-rot fungi (e.g. Xylaria, Annulohypoxylon, Nemania) and various wood-associated endophytes and saprotrophs (Ascocoryne, Trichoderma, Talaromyces). These fungi used a whole range of extracellular lignocellulolytic enzymes, such as peroxidases, peroxide-producing enzymes, laccases, cellulases, glucosidases, hemicellulases (xylanases) and lytic polysaccharide monooxygenases (LPMOs). Both the fungi and enzymes were tree-specific, with specialists and generalists being distinguished by network analysis. The extracellular enzymatic system was highly redundant, with many enzyme classes of different origins present simultaneously in all decaying logs. Strong correlations were found between peroxide-producing enzymes (oxidases) and peroxidases as well as LPMOs, and between ligninolytic, cellulolytic and hemicellulolytic enzymes. The overall protein abundance of lignocellulolytic enzymes was reduced by up to -30% in gymnosperm logs compared to angiosperm logs, and gymnosperms lacked ascomycetous enzymes, which may have contributed to the lower decomposition of gymnosperm wood. In summary, we have obtained a comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in several temperate forest tree species, which can help to improve our understanding of the complex ecological processes in forest ecosystems.
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