ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

Author(s)

Barbosa, David Aciole ^[1] ; Menegidio, Fabiano Bezerra ^[1] ; Alencar, Valquiria Campos ^[1] ; Goncalves, Rafael S. ^[1] ; Santos Silva, Juliana de Fatima ^[1] ; Vilas Boas, Renata Ozelami ^[1] ; Lima Faustino de Maria, Yara Natercia ^[1] ; Jabes, Daniela Leite ^[1] ; de Oliveira, Regina Costa ^[1] ; Nunes, Luiz R. ^[2]

Affiliation

^[1] UMC, Nucleo Integrado Biotecnol, Sao Paulo - Brazil

^[2] Univ Fed ABC, Ctr Ciencias Nat & Humanas, Sao Paulo - Brazil

• Document type: Journal article
• Source: PLoS Neglected Tropical Diseases; v. 13, n. 7 JUL 2019.
• Web of Science Citations: 0

Abstract

Background The genus Paracoccidioides consists of thermodymorphic fungi responsible for Paracoccidioidomycosis (PCM), a systemic mycosis that has been registered to affect similar to 10 million people in Latin America. Biogeographical data subdivided the genus Paracoccidioides in five divergent subgroups, which have been recently classified as different species. Genomic sequencing of five Paracoccidioides isolates, representing each of these subgroups/species provided an important framework for the development of post-genomic studies with these fungi. However, functional annotations of these genomes have not been submitted to manual curation and, as a result, similar to 60-90% of the Paracoccidioides protein-coding genes (depending on isolate/annotation) are currently described as responsible for hypothetical proteins, without any further functional/structural description. Principal findings The present work reviews the functional assignment of Paracoccidioides genes, reducing the number of hypothetical proteins to similar to 25-28%. These results were compiled in a relational database called ParaDB, dedicated to the main representatives of Paracoccidioides spp. ParaDB can be accessed through a friendly graphical interface, which offers search tools based on keywords or protein/DNA sequences. All data contained in ParaDB can be partially or completely downloaded through spreadsheet, multi-fasta and GFF3-formatted files, which can be subsequently used in a variety of downstream functional analyses. Moreover, the entire ParaDB environment has been configured in a Docker service, which has been submitted to the GitHub repository, ensuring long-term data availability to researchers. This service can be downloaded and used to perform fully functional local installations of the database in alternative computing ecosystems, allowing users to conduct their data mining and analyses in a personal and stable working environment. Conclusions These new annotations greatly reduce the number of genes identified solely as hypothetical proteins and are integrated into a dedicated database, providing resources to assist researchers in this field to conduct post-genomic studies with this group of human pathogenic fungi. Author summary The genus Paracoccidioides comprises fungi responsible for Paracoccidioidomycosis (PCM), a neglected tropical disease prevalent in South America that has been shown to affect approximately 10 million people and has great medical/social impact, since available treatments are poorly effective, frequently leading to relapses, chronic infections and sequelae. Genomic information available for five reference Paracoccidioides isolates could greatly assist researchers in developing new chemotherapeutic approaches against PCM, but usefulness of such data is limited, since similar to 60-90% of Paracoccidioides protein-coding genes (depending on isolate) are described as responsible for hypothetical proteins, without any functional/structural description. Such elevated number of hypothetical proteins is unexpected and probably derives from annotations performed solely by automated computing pipelines. This problem can be minimized by manual curation, when expert reviewers determine the functional designation of each gene, after comparing results derived from several reference databases. This work describes an effort to review the functional assignment of >40,000 genes, annotated across the five Paracoccidioides genomes mentioned above, which reduced the number of hypothetical proteins to similar to 25-28%, contributing to significantly increase quality and usefulness of such genomic information. These data have been compiled in a relational database named ParaDB, constituting an important resource for researchers in the field. (AU)

• FAPESP's process: 17/13197-8 - Characterization of promoter elements responsive to the quorum sensing (QS) auto-inducer 2 (AI-2) in Zymomonas mobilis
• Grantee: Luiz Roberto Nunes
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Regular Program Grants
• FAPESP's process: 17/08112-3 - Composition and influence of the intestinal microbiome in mice, during the process of cachexia development, induced by transplantation of Lewis lung carcinoma (LLC) cells
• Grantee: Daniela Leite Jabes
• Support Opportunities: Regular Research Grants