The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis
Abstract
Trichophyton rubrum is the most common etiological agent of dermatophytoses worldwide, which is able to degrade keratinized tissues. The sequencing of the genome of different dermatophyte species has provided a large amount of data, including tandem repeats that may play a role in genetic variability and in the pathogenesis of these fungi. Tandem repeats are adjacent DNA sequences of 2–200 nucleotides in length, which exert regulatory and adaptive functions. These repetitive DNA sequences are found in different classes of fungal proteins, especially those involved in cell adhesion, a determinant factor for the establishment of fungal infection. The objective of this study was to develop a Dermatophyte Tandem Repeat Database (DTRDB) for the storage and identification of tandem repeats in T. rubrum and six other dermatophyte species. The current version of the database contains 35 577 tandem repeats detected in 16 173 coding sequences. The repeats can be searched using entry parameters such as repeat unit length (nt—nucleotide), repeat number, variability score, and repeat sequence motif. These data were used to study the relative frequency and distribution of repeats in the sequences, as well as their possible functions in dermatophytes. A search of the database revealed that these repeats occur in 22–33% of genes transcribed in dermatophytes where they could be involved in the success of adaptation to the host tissue and establishment of infection. The repeats were detected in transcripts that are mainly related to three biological processes: regulation, adhesion, and metabolism. The database developed enables users to identify and analyse tandem repeat regions in target genes related to pathogenicity and fungal–host interactions in dermatophytes and may contribute to the discovery of new targets for the development of antifungal agents. Database URL:http://comp.mch.ifsuldeminas.edu.br/dtrdb/
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“Other specialized databases have been developed recently in this regard (e.g. (122–126)), starting off from human-centered research questions and expanding to examples of many other species, such as the tobacco plant (127), Trichophytum rubrum, a fungus causing skin disease (128), or the Cannabis plant to characterize the origin of hemp seeds (US Cannabis DNA database; (129)).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [128]
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Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
The Pfam protein families database
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Intragenic tandem repeats generate functional variability
Verstrepen, K. J., Jansen, A., Lewitter, F., & Fink, G. R. (2005) · Nature Genetics · doi:10.1038/ng1618 · Cited by 616
Flocculation, adhesion and biofilm formation in yeasts
Verstrepen, K. J., & Klis, F. M. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05072.x · Cited by 589
Selection against frameshift mutations limits microsatellite expansion in coding DNA.
Metzgar, D., Bytof, J., & Wills, C. (2000) · PubMed · Cited by 488
Cited by
Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Metadata
- Authors
- Franco, M. E., Bitencourt, T. A., Marins, M., & Fachin, A. L.
- Affiliations
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-01-01
- Volume
- 2017
- ISSN
- 1758-0463
- PMC
- PMC5502367
- Cited by
- 4
- References
- 35
- Language
- en
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