Furanocoumarins in two European species of Heracleum: transcriptomic and metabolomic study
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PROVIDER: PRJEB85269 | ENA |
REPOSITORIES: ENA
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Project description:In this study, we performed comparative transcriptomics to understand how mechanisms for fungal dimorphism are similar to the model species Ustilago maydis. To achieve this, we selected two non-model species from Ustilaginomycotina, Meira miltonrushii and Tilletiopsis washingtonensis, for transcriptomic profiling. Different culture conditions were used to have these two fungi display yeast growth (Holliday's minimal media with 1% glucose as a carbon source) and filamentous growth (Holliday's minimal media with 1% Tween as a carbon source). Then, we performed transcriptomic sequencing and analyses to determine which genes are differentially expressed in filamentous growth compared to yeast growth. We also incorporated public datasets from other two dimorphic species, U. maydis and Ophiostoma novo-ulmi, for comparison. We found that T. washingtonensis, despite being closely related to M. miltonrushii, is the most distant species in terms of the similarities of transcriptomic alteration, suggesting phylogenetic relatedness may not be concurrent with transcriptomic similarity under the same biological phenomenon. Functional enrichment analyses reveal that genes in cell energy production and conversion, amino acid transport and metabolism and cytoskeleton are groups of genes differentially expressed in common among the four species. Finally, although our comparative approach allows us to discover several candidate genes that may be involved in fungal dimorphism, we found very few commonly expressed genes that are know dimorphism genes characterized in U. maydis literature. This suggests the certain degree of species-specific mechanisms for dimorphic transition.
2021-06-09 | GSE154947 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.
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