Transcriptomic profiling of dimorphic growth in two Ustilaginomycotina species
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ABSTRACT:
PROVIDER: PRJNA647940 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12300423_1.fastq.gz | Fastqsanger.gz | |||
| SRR12300423_2.fastq.gz | Fastqsanger.gz | |||
| SRR12300424_1.fastq.gz | Fastqsanger.gz | |||
| SRR12300424_2.fastq.gz | Fastqsanger.gz | |||
| SRR12300425_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Sexual dimorphism is one of the important topic in mammal species because appearance of males and females is obvious different in all mammal species. In addition to this, molecular mechanisms also very different each other. Furthermore, it is important to employ a variety of tissues in RNA-seq experiment because recent studies imply gene expression pattern are highly tissue specific. Although previous related studies discovered numerous sexually dimorphic mechanism in mammal species, but still, many mechanisms are undiscovered in case of non-model organisms. One of the representative mammal organism is a cattle which is less researched about sexual dimorphism. For investigate bovine sexual dimorphism, we generated two-way factorial designed 40 samples RNA-seq data composed with two factors such as gender and tissues. Two statistical approaches are employed for identifying bovine sexually dimorphic genes using such two-way factorial designed RNA-seq data. As a result, we observed that detected sexually dimorphic genes exhibited strong tissue specific pattern, but fat tissue showed relatively small tissue specificity than the others. In addition, we observed that sex-related genes are shared in two mammal species such as cattle and rat through qRT-PCR experiments. Finally, we investigated pros and cons of two statistical approaches for complex structured RNA-seq analysis.
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