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. 2025 Jan 16;47(1):56.
doi: 10.3390/cimb47010056.

Insights from a Genome-Wide Study of Pantoea agglomerans UADEC20: A Promising Strain for Phosphate Solubilization and Exopolysaccharides Production

Edith Elizondo-Reyna  1 , Humberto Martínez-Montoya  2 , Yahaira Tamayo-Ordoñez  3 , María Antonia Cruz-Hernández  3 , Mauricio Carrillo-Tripp  4 , María Concepción Tamayo-Ordoñez  1 , Gerardo de Jesús Sosa-Santillán  1 , José Antonio Rodríguez-de la Garza  1 , Mario Hernández-Guzmán  5 , Virgilio Bocanegra-García  3 , Erika Acosta-Cruz  1
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Insights from a Genome-Wide Study of Pantoea agglomerans UADEC20: A Promising Strain for Phosphate Solubilization and Exopolysaccharides Production

Edith Elizondo-Reyna et al. Curr Issues Mol Biol. .

Abstract

The genome sequence of Pantoea agglomerans UADEC20 is presented, which is a strain isolated from agricultural fields in northeast Mexico. The genome was assembled into 13 scaffolds, constituting a total chromosome size of 4.2 Mbp, with two of the scaffolds representing closed plasmids. The strain exhibits activity in phosphate solubilization and exopolysaccharide (EPS) production and secretion; therefore, we explored its biotechnological potential via its genome sequencing and annotation. Genomic analyses showed that a total of 57 and 58 coding sequences (CDSs) related to phosphate solubilization and EPS production were identified within its genome, in addition to a reduced number of CDSs related to drug resistance and phages. The comprehensive set of genes supporting phosphate solubilization, EPS synthesis, and secretion, along with its low virulence and antibiotic resistance levels, justify further research for its potential biotechnological application and possible use as a plant growth-promoting agent in the field. These findings suggest a unique genetic background in the P. agglomerans UADEC20 strain.

Keywords: PGPR; Pantoea agglomerans; exopolysaccharide production; genome; phosphate solubilization.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Consensus tree showing the phylogenetic relationship of 21 strains from Pantoea. The final tree was constructed from 2000 bootstrap trees. Pantoea agglomerans UADEC20 is located in Cluster II.
Figure 2
Figure 2
Genome alignments showing synteny blocks of P. agglomerans UADEC20 (top) and P. agglomerans FDAARGOS 1447 (bottom) in Mauve 2.4.0 software. Each genome is presented horizontally with the homologous segment outlined as colored rectangles. Blocks of the same color represent a locally collinear block (LCB) or homologous region shared between the two genomes. The rearrangement of the genomic regions between the two genomes was observed in terms of collinearity; the regions inverted relative to FDAARGOS 1447 are located on the negative strand indicated by the genomic position below the black horizontal center line in the Mauve alignment. Colors indicates similar nucleotide regions between the two chromosomes.
Figure 3
Figure 3
Plasmid 1 of P. agglomerans UADEC20 (top) and plasmid 1 of P. agglomerans FDAARGOS 1447 (bottom) compared using Mauve 2.4.0 software. Colors indicates similar nucleotide regions between the two chromosomes.
Figure 4
Figure 4
Plasmid 2 of P. agglomerans UADEC20 (top) and plasmid 2 of P. agglomerans FDAARGOS 1447 (bottom) compared using Mauve 2.4.0 software. Colors indicates similar nucleotide regions between the two chromosomes.
Figure 5
Figure 5
Plot of the core-/pan-genome and Venn diagram for the core-genome and strain-specific CDSs of the P. agglomerans strains. The outer circles represent the pan-genomes of the different strains and show the conserved (core) and non-conserved (flexible) CDSs for each group. Genes overlapping by at least 80% in length and having 80% similarity were considered orthologs.
Figure 6
Figure 6
Genome comparisons of other P. agglomerans strains against the P. agglomerans UADEC20 draft genome. The black inner circle represents the complete genome of the reference strain UADEC20, and the shade of each color shows the similarities between each one of the strains and that of UADEC20.
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