Hi-C Scaffolding Challenges in Non-Model Lepidoptera

The limited availability of high-quality genomic resources for non-model Lepidoptera severely hampers research on their evolutionary adaptations and restricts their application in biodiversity conservation and agroforestry. This study systematically addresses a critical bottleneck-quality degradation in Hi-C scaffolding-that undermines the structural integrity of Lepidoptera genome assemblies. The findings show that intrinsic genomic features, such as high heterozygosity and abundant repetitive sequences, coupled with technical noise in Hi-C data and algorithmic limitations, frequently lead to large-scale structural errors (including misjoins, inversions, and translocations) that are not easily detected by conventional assembly metrics. To address these challenges, the paper proposes an integrated framework that combines haplotype-resolved assembly, manual curation, and multi-dimensional evaluation. This framework integrates optimized experimental and computational workflows, stringent quality control procedures, and standardized evaluation criteria to establish a comprehensive quality assurance system. Additionally, this paper emphasizes the importance of community collaboration and data transparency in fostering reproducible and scalable genomic research. Together, these advances are expected to significantly enhance the reliability and applicability of genomic resources for non-model Lepidoptera, providing a robust genetic foundation for evolutionary biology, comparative genomics and integrated pest management.