DNA sequence composition affects meiotic recombination. However, the correlation between tandem repeat composition and meiotic recombination in common wheat (Triticum aestivum L.) is unclear. Non-denaturing fluorescent in situ hybridization (ND-FISH) with oligonucleotide (oligo) probes derived from tandem repeats and single-copy FISH were used to investigate recombination in three kinds of the long arm of wheat 5A chromosome (5AL). 5AL535–18/275 arm carries the tandem repeats pTa-535, Oligo-18, and pTa-275, 5AL119.2–18/275 arm carries the tandem repeats pSc119.2, Oligo-18 and pTa-275, and 5AL119.2 arm carries the tandem repeats pSc119.2. In the progeny of 5AL535–18/275 × 5AL119.2, double recombination occurred between pSc119.2 and pTa-535 clusters (119–535 interval), and between pTa-535 and Oligo-18/pTa-275 clusters (535–18 interval). The recombination rate in the 119–535 interval in the progeny of 5AL535–18/275 × 5AL119.2–18/275 was higher than that in the progeny of 5AL535–18/275 × 5AL119.2. Recombination in the 119–535 interval produced 5AL119 + 535 segments with pTa-535 and pSc119.2 tandem repeats and 5ALNo segments without these repeats. The 5AL119 + 535 and 5ALNo segments were localized between the signal sites of the single-copy probes SC5A-479 and SC5A-527. The segment between SC5A-479 and SC5A-527 in the metaphase 5ALNo was significantly longer than that in the metaphase 5AL119 + 535. The structural variations caused by tandem repeats might be one of the factors affecting meiotic recombination in wheat. Meiotic recombination aggregated two kinds of tandemly repeated clusters into the same chromosome, making the metaphase chromosome more condensed. To conclude, our study provides a robust tool to measure meiotic recombination and select parents for wheat breeding programs.

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.

Ribosomal protein S6 kinase (S6K) is a conserved effector of the mTOR signaling pathway that regulates cell growth and metabolism. The organism-level function of S6K in the silkworm Bombyx mori has not yet been examined by direct genetic manipulation. Here, we combined CRISPR/Cas9-mediated knockout, piggyBac-based transgenic re-expression and overexpression, and multi-tissue RNA-seq with weighted gene co-expression network analysis (WGCNA) to characterize the role of BmS6K in vivo. BmS6K-null mutants were viable but showed 26.5% and 28.6% reductions in pupal weight in males and females, respectively. Furthermore, mutant survival rates were 44.2% (males) and 28.5% (females) lower than those of controls, with mortality concentrated at the late fifth larval stage. Targeted transgenic re-expression rescued these phenotypic defects. Conversely, overexpressing BmS6K in a wild-type background increased the larval growth rate by 16.9% and significantly raised both whole cocoon weight and pupal weights. WGCNA of the three tissue types identified a core co-expression module (MEred) that was significantly enriched for genes involved in proton-transporting V-type ATPase activity and vacuolar complex assembly, mTOR signaling, and oxidative phosphorylation coupled to cellular redox homeostasis, including BmV1-ATPase, BmGabaT, and BmNadDac, whose orthologs represent core components or mediate critical cross-talk in the TOR-S6K pathway, a function conserved in Drosophila and mammals. Since the loss and gain of BmS6K produced opposite effects on growth and viability, it can be regarded as a candidate target for increasing cocoon yield in sericulture, as well as a target for RNAi-based control of lepidopteran pests through the suppression of its orthologs.