Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics
<i>Aspergillus</i> spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical b...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/7/4/270 |
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| author | Tim J. H. Baltussen Jordy P. M. Coolen Paul E. Verweij Jan Dijksterhuis Willem J. G. Melchers |
| author_facet | Tim J. H. Baltussen Jordy P. M. Coolen Paul E. Verweij Jan Dijksterhuis Willem J. G. Melchers |
| author_sort | Tim J. H. Baltussen |
| collection | DOAJ |
| description | <i>Aspergillus</i> spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating <i>A. fumigatus</i> and <i>A. niger</i> conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between <i>A. niger</i> and <i>A. fumigatus</i> during conidial germination. Specifically, the <i>turquoise</i> module was enriched with secondary metabolism, the <i>black</i> module was highly enriched with protein synthesis, the <i>darkgreen</i> module was enriched with protein fate, and the <i>blue</i> module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the <i>blue</i> module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in <i>A. fumigatus</i> and <i>A. niger</i>, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by <i>A. fumigatus</i> and <i>A. niger</i>, which underscores the potential of this approach. |
| first_indexed | 2024-03-10T12:40:41Z |
| format | Article |
| id | doaj.art-7a10e8ca1a014a05a6c114ded49eeb42 |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-10T12:40:41Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-7a10e8ca1a014a05a6c114ded49eeb422023-11-21T13:53:36ZengMDPI AGJournal of Fungi2309-608X2021-04-017427010.3390/jof7040270Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species TranscriptomicsTim J. H. Baltussen0Jordy P. M. Coolen1Paul E. Verweij2Jan Dijksterhuis3Willem J. G. Melchers4Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The NetherlandsDepartment of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The NetherlandsDepartment of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The NetherlandsWesterdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The NetherlandsDepartment of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands<i>Aspergillus</i> spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating <i>A. fumigatus</i> and <i>A. niger</i> conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between <i>A. niger</i> and <i>A. fumigatus</i> during conidial germination. Specifically, the <i>turquoise</i> module was enriched with secondary metabolism, the <i>black</i> module was highly enriched with protein synthesis, the <i>darkgreen</i> module was enriched with protein fate, and the <i>blue</i> module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the <i>blue</i> module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in <i>A. fumigatus</i> and <i>A. niger</i>, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by <i>A. fumigatus</i> and <i>A. niger</i>, which underscores the potential of this approach.https://www.mdpi.com/2309-608X/7/4/270aspergillusgerminationconsensusWGCNAisotropic growthpolarized growthRNA-Seq |
| spellingShingle | Tim J. H. Baltussen Jordy P. M. Coolen Paul E. Verweij Jan Dijksterhuis Willem J. G. Melchers Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics Journal of Fungi aspergillus germination consensusWGCNA isotropic growth polarized growth RNA-Seq |
| title | Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics |
| title_full | Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics |
| title_fullStr | Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics |
| title_full_unstemmed | Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics |
| title_short | Identifying Conserved Generic <i>Aspergillus</i> spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics |
| title_sort | identifying conserved generic i aspergillus i spp co expressed gene modules associated with germination using cross platform and cross species transcriptomics |
| topic | aspergillus germination consensusWGCNA isotropic growth polarized growth RNA-Seq |
| url | https://www.mdpi.com/2309-608X/7/4/270 |
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