Characterization of the Full-Length Transcriptome and Regulatory Networks During Quail Skeletal Muscle Development Using Nanopore Sequencing

The quail is a valuable model organism for avian developmental biology and genetic improvement; however, the full-length transcriptomic landscape and regulatory networks underlying critical embryonic developmental stages remain poorly characterized. In this study, we employed Oxford Nanopore Technologies full-length transcriptome sequencing to systematically analyze leg muscle tissues from quail embryos at embryonic day 8 (E8, pre-differentiation stage) and embryonic day 14 (E14, later differentiation stage), with four biological replicates per stage (eight libraries in total). Nanopore sequencing identified a total of 54,938 transcripts and 21,574 genes, including 49,678 known transcripts, 20,980 known genes, 5260 novel transcripts, and 594 novel genes. Analysis of transcriptome structure revealed that alternative first exon and exon skipping represented the predominant stage-specific alternative splicing events, and we identified 2692 lncRNAs. Differential expression analysis identified substantial transcriptome dynamics from E8 to E14, with 5934 differentially expressed transcripts and 3745 differentially expressed genes identified. Functional enrichment analyses, including KEGG, GSEA and PPI network analysis, revealed that the E8 transcriptome was predominantly enriched for pathways associated with cell proliferation, whereas the E14 transcriptome shifted toward the coordinated refinement of myofiber structural assembly and energy metabolism. Here, we present a high-resolution full-length transcriptional atlas of quail skeletal muscle development and identify candidate regulatory genes, offering a valuable theoretical framework and data resource for refining quail genome annotation.