Cuticulome.org: a centralized database of proteins in arthropod cuticles

Abstract

Cuticle proteins, especially the cuticular protein (CP) multigene family, are essential for the building, maintenance, and environmental adaptation of the arthropod exoskeleton. The extensive size of CP repertoire, which often represents 1-2% of the protein-coding genes, is a challenge. The discontinuation of previous centralized databases for CPs and the lack of consistent nomenclature in the field have hindered functional analyses and comparative studies. Here, we present Cuticulome.org (accessible at https://www.Cuticulome.org), a curated knowledgebase of proteins that are found in arthropod cuticles. Database entries include protein sequences, tissue and developmental stage specificity, and diverse functional annotations where available, while implementing a standardized nomenclature system to facilitate intra- and cross-species analyses. At Cuticulome.org, users can download complete taxon-specific cuticular proteomes, entire CP families, or build their own custom datasets defined by taxonomic, protein family, functional, or keyword-based criteria. Cuticulome.org also offers two integrated sequence analysis tools: miniBLAST, which allows users to identify putative orthologous CPs, and Cuticular Protein Classifier, which accurately classifies a protein sequence to an established CP family based on custom Hidden Markov Models. Together, these features establish Cuticulome.org as the new centralized resource for systematic analysis of cuticle proteins.