Dataset Information

LC-MSMS of media agar from co-cultivation of Auricularia cornea and Pseudonocardia mangrovi

ABSTRACT: The co-cultivation investigation showed that A. cornea TBRC 12900 co-cultivated with P. mangrovi TBRC-BCC 42794 showed a high level of A. cornea mycelial growth. Proteomics analysis was employed to reveal predicted biological activities involved in the mutualistic relationship between the two strains during mycelial growth.

INSTRUMENT(S):

ORGANISM(S): Auricularia Cornea Pseudonocardia Mangrovi

SUBMITTER: Paopit Siriarchawatana

LAB HEAD: Paopit Siriarchawatana

PROVIDER: PXD035814 | Pride | 2022-10-27

REPOSITORIES: Pride

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Source:

			Action	DRS
	090221_Swath_CoMushBac_01.mzML	Mzml
	090221_Swath_CoMushBac_01.wiff	Wiff
	090221_Swath_CoMushBac_01.wiff.scan	Wiff
	090221_Swath_CoMushBac_01_Auri.pep.xml	Pepxml
	090221_Swath_CoMushBac_01_Psed.pep.xml	Pepxml

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Project description:The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi. We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences. These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen. The data is available for interactive exploration at http://histo.ucsf.edu. The non-redundant genome sequence of Histoplasma capsulatum G217B was tiled over a set of 93 CombiMatrix arrays, which were then hybridized with labeled cDNA samples from yeast-form (red channel) or mycelial-form (green channel) Histoplasma. Due to low yields from the mycelial samples, only the red channel intensities were analyzed (and the red foreground intensities are, therefore, reported in the VALUE column for each sample). Rather than normalizing intensities across arrays, each probe was evaluated as detected or undetected relative to the negative control intensities on the corresponding array, and the density of detected probes as a function of genome position was used for the remaining analysis.

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LC-MSMS of media agar from co-cultivation of Auricularia cornea and Pseudonocardia mangrovi

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