Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review
Abstract
:1. Introduction
2. Materials and Methods
2.1. Planning
2.2. Execution
- Records were clustered based on their relation to the topic structure using affinity propagation [31] with the R package APCluster, version 1.14.10 [32]. The number of clusters was estimated with the R package NbClust, version 3.0.1 [33], which provides the most frequent best solution among a set of estimates proposed by different criteria.
- Word clouds were generated using the R package wordcloud, version 2.6 [34] based on the paper abstracts of each cluster. This allowed for identification and exclusion of clusters not related to the subject of this review. Before excluding a cluster, some papers were randomly selected, and their titles and abstracts were read first.
- Papers in the selected clusters were subjected to conventional screening using the StArt software.
- After the semiautomated screening, the titles and abstracts were read, and the remaining papers obtained from the databases were read fully to select those for the next step of analysis.
2.3. Summarization
2.4. Bioinformatic Analysis
3. Results
3.1. Bibliometric Analysis
3.2. Characterization of Studies
3.3. Genes and Proteins Associated with Pathogenicity
4. Discussion
4.1. Identification of Studies and Pathogens
4.2. Theobroma cacao Pathogens’ Molecular Characterization
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Questions |
---|
What genera and species of eukaryotic microorganism pathogens of T. cacao have been the focus of omics studies in recent years? |
Which molecular techniques have been applied, and what kind of data are available for each of these species? |
How is scientific production about this subject distributed globally? |
Which scientific journals and subject areas contain the majority of available studies? |
How are the most cited papers found in the systematic review related to each other? |
Which proteins for each species are already associated with pathogenicity in the current literature? |
Do these proteins have orthologs among the T. cacao pathogens discussed in the systematic review? |
Database | String |
---|---|
Scopus | TITLE-ABS-KEY (cocoa OR cacao AND pathogen* OR disease*) AND PUBYEAR > 1999 AND (LIMIT-TO (DOCTYPE, “ar”)) AND (LIMIT-TO (LANGUAGE, “English”)) |
Web of science | TS = (cocoa OR cacao) AND TS = (pathogen* OR disease*) AND Language: (English) AND DOCUMENT TYPE: (Article) |
Paper | Species | Assembly Deposit | Genome Size (Mb) | Number of Gene Models |
---|---|---|---|---|
[13] | M. perniciosa | Genbank: GCA_000183025.1 | 26.7 | 16,329 |
[15] | M. roreri | Genbank: GCA_000488995.1 | 52.2 | 17,910 |
[16] | P. megakarya | Genbank: GCA_002215365.1 | 101.18 | 42,036 |
P. palmivora | Genbank: GCA_002911725.1 | 107.42 | 44,327 | |
[18] | C. cacaofunesta | Genbank: GCA_002776505.1 | 30.5 | 7382 |
[14] | M. perniciosa (MP 4145) + | http://nbcgib.uesc.br/mperniciosa (accessed on 27 April 2023) | 47.01 | 14,210 |
M. roreri | 45.17 | 14,154 | ||
[74] | C. theobromae | Genbank: GCA_009078325.1 | 31.2 | 9264 |
[17] | P. megakarya | http://www.cacaopathogenomics.com/ (accessed on 27 April 2023) | 222.04 ± 25.19 * | 57,577 ± 7904 * |
P. palmivora | 135.32 ± 17.21 * | 36,778 ± 4481 * |
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de Novais, D.P.S.; Batista, T.M.; Costa, E.A.; Pirovani, C.P. Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review. Microorganisms 2023, 11, 1567. https://doi.org/10.3390/microorganisms11061567
de Novais DPS, Batista TM, Costa EA, Pirovani CP. Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review. Microorganisms. 2023; 11(6):1567. https://doi.org/10.3390/microorganisms11061567
Chicago/Turabian Stylede Novais, Diogo Pereira Silva, Thiago Mafra Batista, Eduardo Almeida Costa, and Carlos Priminho Pirovani. 2023. "Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review" Microorganisms 11, no. 6: 1567. https://doi.org/10.3390/microorganisms11061567
APA Stylede Novais, D. P. S., Batista, T. M., Costa, E. A., & Pirovani, C. P. (2023). Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review. Microorganisms, 11(6), 1567. https://doi.org/10.3390/microorganisms11061567