The genus Pseudoxanthomonas was originally described by Finkmann et al. (2000). It encompasses a Gram-negative, aerobic, rod-shaped bacterium that contains ubiquinone-8 (Q-8), and iso-C_15:0 and anteiso-C_15:0 as the major quinone and cellular fatty acids, respectively. The genus was subsequently emended by Thierry et al. (2004) and Lee et al. (2008) as non-endospore-forming, mesophilic, slightly alkalophilic, and either motile or non-motile. Additionally, the genus is oxidase-positive, heterotrophic, and has a DNA G + C content ranging from 65 to 70 mol%. With the growing availability of genomic sequence data, taxonomic classification based on genomes is becoming increasingly complex (Achtman and Wagner, 2008). Currently, 21 species within this genus have been officially reported (Meier-Kolthoff et al., 2022; https://lpsn.dsmz.de/genus/pseudoxanthomonas) and the species Pseudoxanthomonas putridarboris was isolated from a rotten tree (Lee et al., 2017). Its genome sequence has not yet been reported. In this paper, we delineate the draft genome sequence of a type strain Pseudoxanthomonas putridarboris WD12^T (=KACC 15045^T, =LMG 25968^T) isolated from a rotten tree of Korea (Lee et al., 2017).

For the extraction of genomic DNA, P. putridarboris WD12^T was incubated in R2A broth (KisanBio) at 30°C for 18 h and then the genomic DNA was extracted using HiGene^TM Genomic DNA Prep Kit (Biofact) according to the manufacturer’s instructions. The sequencing of genome for P. putridarboris WD12^T was performed by Macrogen Inc. as the Illumina platform with TruSeq Nano DNA (350 bp insert size) library. Raw reads were qualified by FastQC (version 0.11.5) and were assembled by SPAdes (version 3.15.5). Genome completeness and contamination were analyzed with CheckM (Version 1.0.18). The genome annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline, and additional functions of the predicted genes were conducted by the RAST server with the SEED database and BV-BRC web resources. Genomic phylogenetic analysis and digital DNA-DNA hybridization (dDDH) were performed with the Genome-to-Genome Distance calculator resources (Meier-Kolthoff et al., 2022). The overall similarity between the two genome sequences was also measured by OrthoANI (Lee et al., 2016).

The draft genome of P. putridarboris WD12^T consisted of 25 contigs with a total length of 4,227,685 bp and N50 size of 549.3 kb. The sequencing depth of coverage was 144.2 X and the genomic DNA G + C content was 67.5 mol%. The CheckM estimation indicated that genome completeness was 100.0% with 0.55% contamination. A total of 3,681 protein-coding genes, 6 rRNA genes (2 of 5S rRNA, 2 of 16S rRNA, and 2 of 23S rRNA), 49 tRNA genes, 5 non-coding RNA, and 54 pseudogenes were predicted (Table 1).

Table 1

Genome features of Pseudoxanthomonas putridarboris WD12^T

Genome features	Value
No. of scaffolds	25
Depth (X)	144.2
Genome size (bp)	4,227,685
G+C content (%)	67.5
Protein-coding genes	3,681
tRNA genes	49
rRNA genes (5S, 16S, 23S)	6 (2, 2, 2)
Non-coding RNA genes	5
Pseudo genes	54

The genomic phylogenetic tree of P. putridarboris WD12^T formed a cluster with P. mexicana and P. japonensis with a high bootstrap value of 100% (Fig. 1), consistent with the previously established 16S rRNA gene sequence phylogeny (Lee et al., 2017). The dDDH values (formula d₄) between P. putridarboris and P. mexicana, and between P. putridarboris and P. japonensis were 26.6 and 26.3, respectively. The orthoANI values between them were 83.4 and 83.1, respectively.

Fig. 1. Tree inferred with FastME 2.1.6.1 (Lefort et al., 2015) from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d₅. The numbers above branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 90.2%. The tree was rooted at the midpoint (Farris, 1972) and then rerooted with the Lysobacter enzymogenes as an outgroup.

The P. putridarboris WD12^T has been reported to produce extracellular proteases in a previous study (Cho et al., 2010). Two S8 family peptidase genes for extracellular protease precursor (locus-tag AAD027_14980) and extracellular protease (locus-tag AAD027_17475) were identified in its genome. The decomposition of wood requires the breakdown of its components: cellulose, hemicellulose, and lignin (Eriksson et al., 2012). Two genes for β-glucosidases (EC 3.2.1.21, locus-tag AAD027_14365 and locus-tag AAD027_17815), which hydrolyze cellobiose, were present in the genome of P. putridarboris WD12^T. Interestingly, although previous reports indicated that this strain could not hydrolyze xylan, a component of hemicellulose (Lee et al., 2017), the genome contained two genes encoding endo-1,4 β-xylanase (locus tag AAD027_01280, AAD027-13870) and a xylanase precursor (locus tag AAD027_13880). Additionally, a gene of α-L-arabinofuranosidase II (locus tag AAD027_08695) degrading arabinose residues from hemicellulose was present. These enzymes capable of degrading complex organic molecules hold potential value for industrial applications and bio-recycling. They are also expected to play a role in wood decomposition alongside with fungi.

Nucleotide sequence accession numbers

The strain Pseudoxanthomonas putridarboris WD12^T is available at KACC 15045^T, =LMG 25968^T. The draft genome sequence is accessible in GenBank under the accession number JBBWWT000000000. The version described in this paper is Version JBBWWT000000000.1.

국내 부패한 나무에서 분리된 세균 Pseudoxanthomonas putridarboris WD12^T (=KACC 15045^T, =LMG 25968^T)의 초안 유전체 염기서열을 Illumina 플랫폼을 사용하여 결정하였다. 초안 유전체는 총 4,227,685 bp의 길이와 67.5% G + C 함량으로 구성되었으며, 총 3,681개의 단백질 코딩, 6개의 rRNA, 49개의 tRNA 암호화 유전자, 5개의 비암호화 RNA 유전자, 그리고 54개의 유사 유전자를 포함하였다. Pseudoxanthomonas 속의 표준 균주 유전체 서열은 유전체 기반의 분류상에서 기준 유전체로 사용될 수 있다. 또한 생분해성 고분자를 분해하는 세포 외 단백질분해효소, β-glucosidases 및 xylanase를 암호화하는 유전자들은 산업적 응용에 활용될 수 있을 것이다.

This work was supported by a funding for the academic research program of Chungbuk National University in 2024.

The authors have no conflict of interest to report.