The domesticated silkworm (Bombyx mori) is both economically significant and a valuable model organism. However, challenges persist in silk production, particularly in preserving silkworm cocoons. The wild silkworm (Bombyx mandarina), a close relative, with long-term pupal characteristics, could address storage and industrial silk production issues. We conducted interspecies hybridization between domestic and wild silkworms, successfully introducing the long-pupal period trait into the domestic silkworm through genomic integration. Here, we presented the telomere-to-telomere genome assemblies of three silkworm strains (KA, L, and M) with long-term pupal characteristics. The genome assembly sizes ranged from 453.82 Mb to 461.92 Mb, with high contig N50 values and completeness. We predicted over 14,000 protein-coding genes and identified strain-specific fragments. This research enriches the domestic silkworm pan-genome project and provides a foundation for further genetic studies. By introducing the trait, we have for the first time reported a phenomenon of genomic introgression between domestic and wild silkworm, and have also opened up a new avenue for silkworm breeding.

Transcriptome atlases can be used to examine the spatiotemporal dynamics of gene expression, thereby enabling the generation of genome-wide resources for understanding complex biological processes. In the silkworm Bombyx mori, transcriptomes serve as crucial datasets for elucidating the mechanisms underlying economically important traits. In this study, we integrated 832 transcriptome datasets across all developmental stages and tissues and performed whole-genome-scale transcriptome sequencing (RNAseq) on five critical tissues from silkworm strains Xian8 and 9211. We identified 5773 and 3323 housekeeping genes expressed across all developmental stages and tissues, respectively, and these genes were primarily enriched in cellular signaling, transport, structural organization, DNA repair, and RNA processing pathways. We also identified 27 stage-specific genes and 58 tissue-specific genes, providing candidate markers for future single-cell and spatial transcriptomics. A large number of alternative splicing events were detected from 832 NGS samples, indicating the critical roles of alternative splicing in silkworm development. Interestingly, only 10 long-read full-length transcriptome samples from Xian8 and 9211 yielded results comparable to the NGS in terms of novel genes and alternative splicing events, and these multi-tissue comparative analyses also revealed significant differences in alternative splicing patterns, underlining the necessity of long-read sequencing for such research. These datasets not only advance functional genomics research in Lepidoptera but also provide molecular signatures for silkworm strain-specific comparisons and association analyses with differential phenotypes. Silkworm pan-transcriptomics, by analyzing multidimensional transcriptional regulatory networks and gene-expression dynamics, can facilitate multidisciplinary integration and accelerate the breeding of high-yield and high-quality silkworm varieties.

Embryonic diapause is a reversible arrest of embryonic development that enables insects to survive adverse environmental conditions. In the silkworm (Bombyx mori), diapause is established during early egg development and can be efficiently terminated by corona discharge; however, the transcriptional responses associated with this physical stimulus remain insufficiently characterized. Here, we present a strand-specific RNA-seq dataset generated from diapause-destined silkworm eggs subjected to early or late corona discharge treatment. The dataset comprises 36 libraries from three experimental groups across eight developmental time points, with two biological replicates per condition. In total, 283.9 Gb of high-quality clean data were obtained, with average Q20 and Q30 values of 97.60% and 94.20%, respectively, and an average genome-mapping rate of 82.62%. The dataset includes raw reads, gene-expression matrices, lists of differentially expressed genes, novel transcript annotations, alternative splicing events, and SNP/InDel calls. This resource provides a time-resolved transcriptomic framework for investigating physical-stress-induced diapause termination and supports comparative studies of diapause regulation in silkworms and other insects.