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Cited by 4

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

Franco, Matheus Eloy, Bitencourt, Tamires Aparecida, Marins, Mozart, Fachin, Ana Lúcia·2017·Database
DOI 10.1093/database/bax035PMC PMC5502367
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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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Crossref · 10.1093/database/bax035

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Figures

Figure 1. Schematic representation of the architecture of the Dermatophyte Tandem Repeat Database.
Figure 1. Schematic representation of the architecture of the Dermatophyte Tandem Repeat Database.CC BY · PubMed Central
Figure 2. Screens of the web pipeline. (A) Submission form of the fasta file for the identification and storage of repetitive sequences. (B) Query of repeats and functional information of the dermatophyte Trichophyton rubrum. (C) Profile of repeats existing in a certain organism. (D) Query of repeats in an organism using filters.
Figure 2. Screens of the web pipeline. (A) Submission form of the fasta file for the identification and storage of repetitive sequences. (B) Query of repeats and functional information of the dermatophyte Trichophyton rubrum. (C) Profile of repeats existing in a certain organism. (D) Query of repeats in an organism using filters.CC BY · PubMed Central
Figure 3. Distribution of tandem repeats according to repeat unit length (nt).
Figure 3. Distribution of tandem repeats according to repeat unit length (nt).CC BY · PubMed Central
Figure 4. Relative abundance of grouped repeats.
Figure 4. Relative abundance of grouped repeats.CC BY · PubMed Central
Figure 5. Functional categories of genes containing variable tandem repeats.
Figure 5. Functional categories of genes containing variable tandem repeats.CC BY · PubMed Central

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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
DOI
10.1093/database/bax035
PMC
PMC5502367
Cited by
4
References
35
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor, 164 d)

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