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of Phytopathology

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Phylogenomic diversity and genome mining of type Bacillus species: Searching for genes associated with biological control of phytopathogens

By José Jesús Márquez Diego, Andrea Denisse Martinez Vidales, Errikka Patricia Cervantes Enríquez, Abraham Ruiz Castrejón, José Humberto Romero Silva, Maria Edith Ortega Urquieta, Fannie Isela Parra Cota, Sergio de los Santos Villalobos*

* Corresponding Author. Email: / Institution: Instituto Tecnológico de Sonora

Accepted: 19/February/2024 – Published: 06/March/2024 – DOI: https://doi.org/10.18781/R.MEX.FIT.2402-9

Abstract Background/Objective. Bacillus is a cosmopolitan bacterial genus with a great genome diversity. Thus, by exploring its genome background, it is possible to understand more about the physiological and biochemical traits involved in its biological control against phytopathogens. The objective of this work was to correlate the phylogenomic relationships of the type species of the genus Bacillus with the presence of gene clusters associated with biological control of plant pathogens, through genome mining.

Materials and Methods. Based on the literature, 336 species belonging to the genus Bacillus have been reported; however, after re-classification, a total of 123 type species have been recognized, and curated genomes were found in the EzBioCloud platform (http://www.ezbiocloud.net/). The overall genome relatedness indices (OGRIs) were used for this work, which indicate how similar two sequences of a genome are. Then, the Realphy platform was used to create the phylogenomic tree 1.13 (Action-based phylogeny constructor reference). Finally, the prediction of biosynthetic gene clusters (BGC) associated with the biological control of phytopathogens was carried out using antiSMASH v6.0 (https://antismash. secondarymetabolites.org/).

Results. The present strategy allowed us to correlate and predict the biological control capacity of the Bacillus species under study based on their taxonomic affiliation since at a shorter evolutionary distance from Bacillus subtilis a high potential capacity to produce biological control compounds was observed. However, the possibility that they acquire the ability to produce new biocontrol compounds during their evolutionary separation is not ruled out.

Conclusion. This work validates the correlation between the taxonomic affiliation of the studied Bacillus species and their biological control capacity, which is useful in the bioprospecting stage to design promising biopesticides.

Keywords: Biocontrol, Genome mining, Bacillus, AntiSMASH, Taxonomy

Figure 1. Phylogenomic tree with the 123 studied type <em>Bacillus</em> species, where two main groups were identified: i) B. megaterium (pink color) and ii) B. subtilis (blue color)
Figure 1. Phylogenomic tree with the 123 studied type Bacillus species, where two main groups were identified: i) B. megaterium (pink color) and ii) B. subtilis (blue color)
Table 1. Type strain species belonging to the genus <em>Bacillus</em> downloaded from the EzBioCloud platform, which were used in this study
Table 1. Type strain species belonging to the genus Bacillus downloaded from the EzBioCloud platform, which were used in this study