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The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
Open accessAbstract
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community. In addition to being a repository and central point of access to genome, transcriptome and polymorphism data, AspGD hosts a comprehensive comparative genomics toolbox that facilitates the exploration of precomputed orthologs among the 20 currently available Aspergillus genomes. AspGD curators perform gene product annotation based on review of the literature for four key Aspergillus species: Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus and Aspergillus niger. We have iteratively improved the structural annotation of Aspergillus genomes through the analysis of publicly available transcription data, mostly expressed sequenced tags, as described in a previous NAR Database article (Arnaud et al. 2012). In this update, we report substantive structural annotation improvements for A. nidulans, A. oryzae and A. fumigatus genomes based on recently available RNA-Seq data. Over 26 000 loci were updated across these species; although those primarily comprise the addition and extension of untranslated regions (UTRs), the new analysis also enabled over 1000 modifications affecting the coding sequence of genes in each target genome.
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Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
Nierman, W. C., Pain, A., Anderson, M. J., Wortman, J. R., Kim, H. S., Arroyo, J., Berriman, M., Abe, K., Archer, D. B., Bermejo, C., et al. (2005) · Nature · doi:10.1038/nature04332 · Cited by 1,391
Self-citationInglis, D. O., Binkley, J., Skrzypek, M. S., Arnaud, M. B., Cerqueira, G. C., Shah, P., Wymore, F., Wortman, J. R., & Sherlock, G. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-91 · Cited by 293
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Aspergillus fumigatus and Aspergillosis in 2019
Latgé, J.-P., & Chamilos, G. (2019) · Clinical Microbiology Reviews · doi:10.1128/cmr.00140-18 · Cited by 1,400
Interactions of Aspergillus fumigatus Conidia with Airway Epithelial Cells: A Critical Review
Croft, C. A., Culibrk, L., Moore, M. M., & Tebbutt, S. J. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00472 · Cited by 142
Role of Hydrophobins in Aspergillus fumigatus
Valsecchi, I., Dupres, V., Stephen-Victor, E., Guijarro, J., Gibbons, J., Beau, R., Bayry, J., Coppee, J.-Y., Lafont, F., Latgé, J.-P., et al. (2017) · Journal of Fungi · doi:10.3390/jof4010002 · Cited by 123
Gacek-Matthews, A., Berger, H., Sasaki, T., Wittstein, K., Gruber, C., Lewis, Z. A., & Strauss, J. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006222 · Cited by 105
Wiemann, P., Perevitsky, A., Lim, F. Y., Shadkchan, Y., Knox, B. P., Landero Figueora, J. A., Choera, T., Niu, M., Steinberger, A. J., Wüthrich, M., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.04.019 · Cited by 104
Metadata
- Authors
- Cerqueira, G. C., Arnaud, M. B., Inglis, D. O., Skrzypek, M. S., Binkley, G., Simison, M., Miyasato, S. R., Binkley, J., Orvis, J., Shah, P., Wymore, F., Sherlock, G., & Wortman, J. R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-04
- Volume
- 42
- Issue
- D1
- Pages
- D705-D710
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2062946300
- Cited by
- 253
- References
- 2
- FWCI
- 10.09
- Type
- journal article
- Language
- en
- Open access
- gold
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