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Journals / Türk Tarım ve Doğa Bilimleri Dergisi / 2025 / Volume: 12 Issue: 4

Genome-wide Identification of the Chitinase and Nonenzymatic Chitinase-Like (Idgf) Genes in Drosophila suzukii (Diptera: Drosophilidae)

Tuğberk Tunçyürek(CANAKKALE ONSEKIZ MART UNIVERSITY)0009-0002-4478-5834
Uğur Sarı(CANAKKALE ONSEKIZ MART UNIVERSITY)0000-0001-7564-997X
Hanife Genç(ÇANAKKALE ONSEKİZ MART ÜNİVERSİTESİ)0000-0001-8180-4307
Pages
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Publication Date
2025-10-17
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

These findings provide the first comprehensive overview of the chitinase and chitinase-like gene family in D. suzukii, laying a foundation for further functional characterization studies and potential pest management strategies targeting chitin metabolic pathways.

📌 3 Key Takeaways

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Objective & Hypothesis:Drosophila suzukii (Spotted-winged drosophila) is an invasive fruit pest in Türkiye.
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Key Findings & Data:Chitinases (Cht) are glycoside hydrolase 18 family enzymes that degrade chitin, while imaginal disc growth factors (Idgf) are non-enzymatic chitinase-like proteins vital for insect development.
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Conclusion & Impact:These findings provide the first comprehensive overview of the chitinase and chitinase-like gene family in D. suzukii, laying a foundation for further functional characterization studies and potential pest management strategies targeting chitin metabolic pathways.
🔬Design:Modeling & Simulation
📍Scope:Comprehensive Sample
⚙️Variables:Drosophila suzukii · chitinases · imaginal disc grwoth factors

Abstract

Drosophila suzukii (Spotted-winged drosophila) is an invasive fruit pest in Türkiye. Chitinases (Cht) are glycoside hydrolase 18 family enzymes that degrade chitin, while imaginal disc growth factors (Idgf) are non-enzymatic chitinase-like proteins vital for insect development. However, chitinase and chitinase-like genes have not yet been identified in the D. suzukii genome, and limited information is available about them. In this study, a comprehensive genome-wide analysis of the Cht and Idgf genes in D. suzukii was performed using a bioinformatics approach. Fifteen genes (11 Cht and 4 Idgf) were identified in the D. suzukii genome, and their sequences, domain structures, and phylogenetic relationships were characterized. Gene structure analysis revealed considerable diversity in exon-intron organization and gene lengths. Fifteen conserved protein motifs were analyzed, and motifs 1, 6, and 8 were detected in all members and others unique to subsets of genes, highlighting both shared and specialized functional regions. Cis-regulatory elements analysis uncovered 543 cis-regulatory elements (including core promoters, stress-responsive elements, enhancers/silencers, and insulators), suggesting complex regulation of these genes. A protein–protein interaction network analysis grouped the Cht/Idgf proteins into three clusters, with DsCht2, DsCht5-2, and DsCht7 emerging as central nodes in chitin metabolism pathways. 3D structural models were predicted for all proteins, and it was determined that the model confidence scores for the proteins varied. In addition, it was confirmed that the catalytic domain features were conserved for these proteins. Finally, RNA-Seq expression profiles showed tissue-specific expression patterns, notably high expression of DsIdgf4 in antennae and DsCht7 in multiple tissues, implying roles in sensory function and chitin metabolism. These findings provide the first comprehensive overview of the chitinase and chitinase-like gene family in D. suzukii, laying a foundation for further functional characterization studies and potential pest management strategies targeting chitin metabolic pathways.

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Cite This Article

Tunçyürek, T., Sarı, U., Genç, H. (2025). Genome-wide Identification of the Chitinase and Nonenzymatic Chitinase-Like (Idgf) Genes in Drosophila suzukii (Diptera: Drosophilidae). Türk Tarım ve Doğa Bilimleri Dergisi, Volume: 12 Issue: 4. https://doi.org/10.30910/turkjans.1750042

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References (52)

  1. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., George, R. A., Lewis, S. E., Richards, S., Ashburner, M., Henderson, S. N., Sutton, G. G., Wortman, J. R., Yandell, M. D., Zhang, Q., … Venter, J. C. (2000). The genome sequence of Drosophila melanogaster. Science, 287(5461), 2185–2195.
  2. Ahn, S. J., Oh, H. W., Corcoran, J., Kim, J. A., Park, K. C., Park, C. G., & Choi, M. Y. (2020). Sex biased gene expression in antennae of Drosophila suzukii. Archives of Insect Biochemistry and Physiology, 104, e21689.
  3. An, S., Liu, W., Fu, J., Zhang, Z., & Zhang, R. (2023). Molecular identification of the chitinase genes in Aedes albopictus and essential roles of AaCht10 in pupal–adult transition. Parasites & Vectors, 16(1), 120.
  4. Arakane, Y., & Muthukrishnan, S. (2010). Insect chitinase and chitinase-like proteins. Cellular and Molecular Life Sciences, 67(2), 201–216.
  5. Asplen, M. K., Anfora, G., Biondi, A., Choi, D.-S., Chu, D., Daane, K. M., Gibert, P., Gutierrez, A. P., Hoelmer, K. A., Hutchison, W. D., Isaacs, R., Jiang, Z.-L., Kárpáti, Z., Kimura, M. T., Pascual, M., Philips, C. R., Plantamp, C., Ponti, L., Vétek, G., Vogt, H., Walton, V.M., Yu, Y., Zappala, L., & Desneux, N. (2015). Invasion biology of spotted wing Drosophila (Drosophila suzukii): A global perspective and future priorities. Journal of Pest Science, 88(3), 469–494.
  6. Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME Suite. Nucleic Acids Research, 43(W1), W39–W49.
  7. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242.
  8. Bruck, D. J., Bolda, M., Tanigoshi, L., Klick, J., Kleiber, J., Defrancesco, J., Gerdeman, B., & Spitler, H. (2011). Laboratory and field comparisons of insecticides to reduce infestation of Drosophila suzukii in berry crops. Pest Management Science, 67(11), 1375–1385.
  9. Bryant, P. J. (2001). Growth factors controlling imaginal disc growth in Drosophila. In D. J. Chadwick & J. A. Goode (Eds.), The Cell Cycle and Development (Novartis Foundation Symposium 237, pp. 182–199). John Wiley & Sons, Ltd.
  10. Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2023). TBtools II: A “one for all, all for one” bioinformatics platform for biological big data mining. Molecular Plant, 16(6), 1733–1742.
  11. Chen, L., Liu, T., Zhou, Y., Chen, Q., Shen, X., & Yang, Q. (2014). Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting. Acta Crystallographica Section D: Biological Crystallography, 70(4), 932–942.
  12. Chen, Y., Tang, H., Zhou, W., Li, C., Chen, Y. N., Zhang, Q., Fu, K. Y., Guo, W. C., & Shi, J. F. (2024). Identification of chitinase genes and roles in the larval–pupal transition of Leptinotarsa decemlineata. Pest Management Science, 80(2), 282–295.
  13. Cheng, X., Zhou, Q., Xiao, J., Qin, X., Zhang, Y., Li, X., Zheng, W., & Zhang, H. (2024). Nanoparticle LDH enhances RNAi efficiency of dsRNA in piercing-sucking pests by promoting dsRNA stability and transport in plants. Journal of Nanobiotechnology, 22(1), 544.
  14. Cohen, E. (2010). Chitin biochemistry: Synthesis, hydrolysis and inhibition. In Advances in Insect Physiology (Vol. 38, pp. 5–74). Academic Press.
  15. Dillon, S. C., Zhang, X., Trievel, R. C., & Cheng, X. (2005). The SET-domain protein superfamily: Protein lysine methyltransferases. Genome Biology, 6(8), 227.
  16. Drosopoulou, E., Gariou-Papalexiou, A., Karamoustou, E., Christopoulou, A., Mavragani-Tsipidou, P., & Iatrou, K. (2019). The chromosomes of Drosophila suzukii (Diptera: Drosophilidae): Detailed photographic polytene chromosomal maps and in situ hybridization data. Molecular Genetics and Genomics, 294(6), 1535–1546.
  17. Dukariya, G., & Kumar, A. (2020). Distribution and biotechnological applications of chitinase: A review. International Journal of Biochemistry and Biophysics, 8(1), 17–29.
  18. Gagneux, P. (2003). Review of the book Gene Regulation: A Eukaryotic Perspective (4th ed., 368 pp.), by D. S. Latchman. Journal of Heredity, 94(6), 528–529.
  19. Gu, X., Li, Z., Su, Y., Zhao, Y., & Liu, L. (2019). Imaginal disc growth factor 4 regulates development and temperature adaptation in Bactrocera dorsalis. Scientific Reports, 9(1), 931.
  20. Guillén, D., Sánchez, S., & Rodríguez-Sanoja, R. (2010). Carbohydrate binding domains: Multiplicity of biological roles. Applied Microbiology and Biotechnology, 85(6), 1241–1249.
  21. Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics, 31(8), 1296–1297.
  22. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., & von Mering, C. (2009). STRING 8—A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37(Database issue), D412–D416.
  23. Kadonaga, J. T. (2012). Perspectives on the RNA polymerase II core promoter. Wiley Interdisciplinary Reviews: Developmental Biology, 1(1), 40–51.
  24. Karlsson, M., & Stenlid, J. (2009). Evolution of family 18 glycoside hydrolases: Diversity, domain structures and phylogenetic relationships. Journal of Molecular Microbiology and Biotechnology, 16(4), 208–223.
  25. Kawamura, K., Shibata, T., Saget, O., Peel, D., & Bryant, P. J. (1999). A new family of growth factors produced by the fat body and active on Drosophila imaginal disc cells. Development, 126(1), 211–219.
  26. Kramer, K. J., & Koga, D. (1986). Insect chitin: Physical state, synthesis, degradation and metabolic regulation. Insect Biochemistry, 16(6), 851–877.
  27. Kramer, K. J., Hopkins, T. L., & Schaefer, J. (1988). Insect cuticle structure and metabolism. In P. A. Hedin, J. J. Menn, & R. M. Hollingworth (Eds.), ACS Symposium Series (Vol. 379, pp. 160–185). American Chemical Society.
  28. Liu, S. H., Li, H. F., Yang, Y., Yang, R. L., Yang, W. J., Jiang, H. B., Dou, W., Smagghe, G., & Wang, J. J. (2018). Genome-wide identification of chitinase and chitin deacetylase gene families in the oriental fruit fly, Bactrocera dorsalis (Hendel). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 27, 13–22.
  29. Liu, T., Guo, X., Bu, Y., Zhou, Y., Duan, Y., & Yang, Q. (2020). Structural and biochemical insights into an insect gut-specific chitinase with antifungal activity. Insect Biochemistry and Molecular Biology, 119, 103342.
  30. Merzendorfer, H. (2006). Insect chitin synthases: A review. Journal of Comparative Physiology B, 176(1), 1–15. Merzendorfer, H., & Zimoch, L. (2003). Chitin metabolism in insects: Structure, function and regulation of chitin synthases and chitinases. Journal of Experimental Biology, 206(24), 4393–4412.
  31. Nakabachi, A., Shigenobu, S., & Miyagishima, S. (2010). Chitinase-like proteins encoded in the genome of the pea aphid, Acyrthosiphon pisum. Insect Molecular Biology, 19(2), 175–185.
  32. Partridge, L., Alic, N., Bjedov, I., & Piper, M. D. (2011). Ageing in Drosophila: The role of the insulin/Igf and TOR signalling network. Experimental Gerontology, 46(5), 376–381.
  33. Peng, Z., Ren, J., Su, Q., Zeng, Y., Tian, L., Wang, S., Wu, Q., Liang, P., Xie, W., & Zhang, Y. (2021). Genome-wide identification and analysis of chitinase-like gene family in Bemisia tabaci (Hemiptera: Aleyrodidae). Insects, 12(3), 254.
  34. Rabadiya, D., & Behr, M. (2024). The biology of insect chitinases and their roles at chitinous cuticles. Insect Biochemistry and Molecular Biology, 165, 104058.
  35. Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738.
  36. Rudall, K. M., & Kenchington, W. (1973). The chitin system. Biological Reviews, 48(4), 597–636. Shawer, R. (2021). Chemical control of Drosophila suzukii. In Drosophila suzukii Management (pp. 133–142). Springer.
  37. Shippy, T., Miller, S., Tamayo, B., Hosmani, P., Flores Gonzalez, M., Mueller, L., Hunter, W., Brown, S., D’Elia, T., & Saha, S. (2022). Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri. Gigabyte, 1–17.
  38. Sustar, A. E., Strand, L. G., Zimmerman, S. G., & Berg, C. A. (2023). Imaginal disk growth factors are Drosophila chitinase-like proteins with roles in morphogenesis and CO₂ response. Genetics, 223(1), iyad161.
  39. Vihervaara, A., Duarte, F. M., & Lis, J. T. (2018). Molecular mechanisms driving transcriptional stress responses. Nature Reviews Genetics, 19(6), 385–397.
  40. Vincent, J. F. V., & Wegst, U. G. K. (2004). Design and mechanical properties of insect cuticle. Arthropod Structure & Development, 33(3), 187–199.
  41. Wang, Y., Farine, J. P., Yang, Y., Yang, J., Tang, W., Gehring, N., Ferveur, J. F., & Moussian, B. (2020). Transcriptional control of quality differences in the lipid-based cuticle barrier in Drosophila suzukii and Drosophila melanogaster. Frontiers in Genetics, 11, 887.
  42. Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Prüß, M., Reuter, I., & Schacherer, F. (2000). TRANSFAC: An integrated system for gene expression regulation. Nucleic Acids Research, 28(1), 316–319.
  43. Wu, Z.-Z., Zhang, W.-Y., Lin, Y.-Z., Li, D.-Q., Shu, B.-S., & Lin, J.-T. (2022). Genome-wide identification, characterization and functional analysis of the chitinase and chitinase-like gene family in Diaphorina citri. Pest Management Science, 78(11), 3287–3300.
  44. Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43(W1), W174–W181.
  45. Yang, J., Ramos, E., & Corces, V. G. (2012). The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species. Genome Research, 22(11), 2199–2207.
  46. Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8.
  47. Yu, A., Beck, M., Merzendorfer, H., & Yang, Q. (2024). Advances in understanding insect chitin biosynthesis. Insect Biochemistry and Molecular Biology, 164, 104058.
  48. Yu, H. Z., Li, N. Y., Xie, Y. X., Zhang, Q., Wang, Y., & Lu, Z. J. (2020). Identification and functional analysis of two chitin synthase genes in the common cutworm, Spodoptera litura. Insects, 11(4), 253.
  49. Yu, R. R., Liu, W. M., Zhao, X. M., Zhang, M., Li, D. Q., Zuber, R., Ma, E. B., Zhu, K. Y., Moussian, B., & Zhang, J. Z. (2019). LmCDA1 organizes the cuticle by chitin deacetylation in Locusta migratoria. Insect Molecular Biology, 28(3), 301–312.
  50. Zhang, C., He, L., Ding, B., & Yang, H. (2024). Identification and functional characterization of the chitinase and chitinase-like gene family in Myzus persicae (Sulzer) during molting. Pest Management Science, 81(2), 327–339.
  51. Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40. Zhao, K., Hart, C. M., & Laemmli, U. K. (1995). Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell, 81(6), 879–889.
  52. Zhu, Q., Deng, Y., Vanka, P., Brown, S. J., Muthukrishnan, S., & Kramer, K. J. (2004). Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. Bioinformatics, 20(2), 161–169.