Full-Length Transcriptome Sequencing of Multiple Tissues from silkworm '9211' and 'Xian 8'
Transcriptome atlases provide spatiotemporal molecular characterizations of gene expression dynamics, enabling the generation of rich genome-wide resources for understanding complex biological processes in organisms like silkworm, Bombyx mori, and serve as crucial datasets for elucidating molecular mechanisms. Here, we integrated 832 public transcriptome datasets across all developmental stages and tissues and performed whole-genome-scale transcriptome sequencing on 5 critical tissues from market strain Xian8 and 9211. We identified 5,772 and 3,323 housekeeping genes constitutively expressed throughout all development stages and tissues respectively, and these genes main enriched in cellular signaling, transport, structural organization, and DNA repair, RNA processing pathways. We also identified 27 development-stage-specific genes and 57 tissue-specific genes, providing candidate marker genes for future single cell transcriptomics and spatial transcriptomics. Large number of alternative splicing events and differential alternative splicing events were detected from 832 NGS samples, indicating the critical roles of alternative splicing in silkworm development. Interestingly, only ten long-read full-length transcriptome samples from Xian18 and 9211 revealed comparable numbers to NGS results via novel genes and alternative splicing events, and these multi-tissue comparative analyses also revealed significant differences in alternative splicing patterns, underlining the necessary of long-read sequencing for such research field. These datasets not only advance functional genomics research in Lepidoptera, but also provide molecular signatures for silkworm strain-specific comparisons and association analysis with differential phenotypes. Silkworm pan-transcriptomics, through analyzing multi-dimensional transcriptional regulatory networks and gene expression dynamics, will promote multidisciplinary integration, and will accelerate the breeding process for high-yield and high-quality silkworm varieties.