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

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.