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Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum

Sayı: 2026 27 Ekim 2026
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Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum

Öz

Xenorhabdus szentirmaii is a symbiotic bacterium of entomopathogenic Steinernema nematodes and a promising source of bioactive specialized metabolites. In this study, the genome of X. szentirmaii PAM25, isolated from Steinernema rarum PAM25, was sequenced to evaluate biosynthetic potential. Whole-genome sequencing generated a 4.68-Mb draft genome comprising 120 contigs, with 44% GC content, and 3992 predicted coding sequences. Biosynthetic mining with antiSMASH detected 18 biosynthetic gene clusters in X. szentirmaii PAM25, including NRPS, phenazine, siderophore, arylpolyene, RiPP, terpene, betalactone, and hybrid clusters, with high-similarity matches to fabclavine, iodinin, aerobactin, and aryl polyenes. GECCO and SanntiS supported the major biosynthetic predictions. BiG-SCAPE analysis showed that most clusters belonged to gene cluster families conserved across X. szentirmaii, whereas several NRPS-associated loci displayed accessory distributions. Notably, region 40.2, predicted as an NRPS–furan hybrid, formed an X. szentirmaii PAM25-specific singleton gene cluster family. Region 40.2 largely overlapped a predicted genomic island containing both biosynthetic cores and mobility-associated genes. These findings expand genomic knowledge of X. szentirmaii and reveal a largely conserved but partially strain-specific biosynthetic repertoire with potential for specialized-metabolite discovery.

Anahtar Kelimeler

Xenorhabdus szentirmaii, whole-genome sequencing, genome mining, biosynthetic gene cluster

Kaynakça

  1. Akhurst, R. J. (1980). Morphological and functional dimorphism in Xenorhabdus spp., bacteria symbiotically associated with the insect pathogenic nematodes Neoaplectana and Heterorhabditis. Microbiology, 121(2), 303–309. doi:10.1099/00221287-121-2-303
  2. Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Retrieved from http://www.bioinformatics.babraham.ac.uk/proje cts/fastqc/
  3. Bertelli, C., Laird, M. R., Williams, K. P., Lau, B. Y., Hoad, G., Winsor, G. L., & Brinkman, F. S. L. (2017). IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research, 45(W1), W30–W35. doi:10.1093/nar/gkx343
  4. Blin, K., Shaw, S., Vader, L., Szenei, J., Reitz, Z. L., Augustijn, H. E., … Weber, T. (2025). antiSMASH 8.0: Extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation. Nucleic Acids Research, 53(W1), W32–W38. doi:10.1093/nar/gkaf334
  5. Bode, H. B. (2009). Entomopathogenic bacteria as a source of secondary metabolites. Current Opinion in Chemical Biology, 13(2), 224–230. doi:10.1016/j.cbpa.2009.02.037
  6. Brachmann, A. O., Forst, S., Furgani, G. M., Fodor, A., & Bode, H. B. (2006). Xenofuranones A and B: Phenylpyruvate dimers from Xenorhabdus szentirmaii. Journal of Natural Products, 69(12), 1830–1832. doi:10.1021/np060409n
  7. Carattoli, A., Zankari, E., García-Fernández, A., Larsen, M. V., Lund, O., Villa, L., … Hasman, H. (2014). In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrobial Agents and Chemotherapy, 58(7), 3895–3903. doi:10.1128/AAC.02412-14
  8. Carroll, L. M., Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio, E., & Zeller, G. (2021). Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv, 2021.05.03.442509. doi:10.1101/2021.05.03.442509
  9. Chacón-Orozco, J. G., Bueno, C. J., Shapiro-Ilan, D. I., Hazir, S., Leite, L. G., & Harakava, R. (2020). Antifungal activity of Xenorhabdus spp. and Photorhabdus spp. against the soybean pathogenic Sclerotinia sclerotiorum. Scientific Reports, 10(1), 20649. doi:10.1038/s41598-020- 77472-6
  10. Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. doi:10.1093/bioinformatics/bty560

Kaynak Göster

APA
Kalındamar, Ş. (2026). Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum. Journal of Anatolian Environmental and Animal Sciences, 2026. https://doi.org/10.35229/jaes.2029755
AMA
1.Kalındamar Ş. Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum. Journal of Anatolian Environmental and Animal Sciences. 2026;(2026). doi:10.35229/jaes.2029755
Chicago
Kalındamar, Şafak. 2026. “Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum”. Journal of Anatolian Environmental and Animal Sciences, sy 2026. https://doi.org/10.35229/jaes.2029755.
EndNote
Kalındamar Ş (01 Ekim 2026) Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum. Journal of Anatolian Environmental and Animal Sciences 2026
IEEE
[1]Ş. Kalındamar, “Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum”, Journal of Anatolian Environmental and Animal Sciences, sy 2026, Eki. 2026, doi: 10.35229/jaes.2029755.
ISNAD
Kalındamar, Şafak. “Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum”. Journal of Anatolian Environmental and Animal Sciences. 2026 (01 Ekim 2026). https://doi.org/10.35229/jaes.2029755.
JAMA
1.Kalındamar Ş. Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum. Journal of Anatolian Environmental and Animal Sciences. 2026. doi:10.35229/jaes.2029755.
MLA
Kalındamar, Şafak. “Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum”. Journal of Anatolian Environmental and Animal Sciences, sy 2026, Ekim 2026, doi:10.35229/jaes.2029755.
Vancouver
1.Şafak Kalındamar. Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum. Journal of Anatolian Environmental and Animal Sciences. 01 Ekim 2026;(2026). doi:10.35229/jaes.2029755