## 3 Results and Discussion
### Pseudomonas jordanii Strain G34 Genome Insight  
_Pseudomonas jordanii_ strain G34's draft genome comprised 30 contigs with a collective length of 5,142,528 bp, featuring a G + C content of 64.01% and an N50 value of 353,980 bp (Table S1). The predicted number of coding genes was 4766, including 57 RNA coding genes and 4675 protein-coding genes, with the RNA coding genes consisting of 54 _transfer RNAs_ (_tRNAs_) and 3 _rRNAs_. Taxonomic analysis based on whole-genome sequencing indicated a close relationship between _P. jordanii_ strain G34 and _P. argentinensis_ LMG22563, with a shared digital DNA-DNA hybridization (dDDH) identity of 40.2%, as shown in Figure 3A. This finding is supported by comparing genomic signatures, emphasizing the novelty of _P. jordanii_ strain G34 as a distinct species and highlighting its promising potential as a biofertilizer, similar to _P. argentinensis_ LMG22563. A pangenome analysis was carried out to assess the differences between _P. jordanii_ strain G34 and the closely related species revealed through whole-genome alignment (shown in the phylogenetic trees of Figure 3). The analysis covers all genes within a group of related organisms that are classified by sequence homology. At first, specific gene clades were identified by comparing the genomes of _P. jordanii_ strain G34 with _P. argentinensis_ LMG22563, using _P. stutzeri_ as an outgroup (Figure 4A). Later on, the comparison was  
Figure 3: (**A**) Phylogenetic tree based on whole-genome sequences; species clusters are indicated with corresponding color codes, the GC% is represented in the blue color intensity. The genome size is indicated by a black bar and the protein count are represented by the brown bars, respectively. (**B**) The genomic signatures-based phylogenetic tree showing octanucleotides frequencies along the scale beneath the tree. broadened to encompass all 21 closely related species identified during the whole-genome alignment step (Figure 4B). The Pang genome analysis revealed significant differences, especially the abundance of unique sequences (base singletons) between _P. jordanii_ strain G34 and _P. argentinensis_ LMG22563, reinforcing the classification of _P. jordanii_ strain G34 as a distinct species. This genomic divergence is significant in elucidating the distinct characteristics and potential applications of strain G34, particularly in enhancing plant growth under stress conditions [44]. The prevalence of unique sequences in _P. jordanii_ strain G34 suggests specialized adaptations that could be harnessed for the development of agricultural biofertilizers, akin to other beneficial _Pseudomonas_ species [45]. RASTtk annotation, available through the PATRIC server [26], was utilized to classify the functional genes in _P. jordanii_ strain G34. Among the annotated genes, 992 were hypothetical proteins, while 3764 had functional assignments (Table S2). Of these, 1126 were assigned Enzyme Commission (EC) numbers, 961 had Gene Ontology (GO) assignments, and 849 were mapped to KEGG pathways [46; 47; 48]. Furthermore, the annotation revealed 4516 proteins belonging to cross-genus protein families (PGFams) and 4485 proteins belonging to genus-specific protein families (PLFams) [49]. In addition, four CRISPR systems were identified in _P. jordanii_ strain G34 (Table S3). Intriguingly, the genome of _P. argentinensis_ LMG22563 lacks a CRISPR system entirely. The classification of CRISPR-Cas variants is deemed significant in comparative genomic analysis for understanding the evolutionary relationships among related species [50]. The annotation analysis revealed a substantial number of predicted genes involved in carbohydrate metabolism, encompassing pathways for fructose, xylose, and the biosynthesis of menaquinone and quinone cofactors. These genes hold potential as alternative electron transporters in photosynthesis, potentially acting as vital redox molecules (Figure 5). Moreover, genes linked to nitrogen, phosphate, sulfur, iron, and sodium acquisition were detected.