PacBio Single-Molecule Long-Read Transcriptome Sequencing and Analysis of Somatic Embryogenesis in Picea mongolica

Jinling DaiShengli ZhangYu'e Bai^*

• Inner Mongolia Agricultural University, Hohhot, China

Picea mongolica, an endangered conifer species endemic to Hunshandak Sandy Land, has a unique ecological adaptation to extreme desert conditions. This species faces critical conservation challenges owing to its slow regeneration rates, limited seed production, and high susceptibility to pathogens, which collectively threaten population sustainability and genetic diversity. To address these challenges, we conducted long-read transcriptome sequencing using the PacBio SMRT technology on pooled samples representing various stages of somatic embryogenesis. Our analyses yielded 12,232 high-quality transcripts. The obtained transcripts were functionally annotated using four major databases, Nr, SwissProt, KEGG, and KOG. A detailed examination of transcript features identified 83 genes with alternative splicing patterns, 1,006 SSR loci, 35 lncRNAs, and 548 transcription factors spanning 46 distinct families. The BABY BOOM (BBM) gene, a member of the AP2/ERF transcription factor family, serves as a molecular marker during plant embryogenesis. It plays multifaceted roles in plant growth and development, including promoting cell proliferation and regeneration, enhancing genetic transformation efficiency, inducing adventitious root formation, and facilitating apomixis. We successfully cloned and characterized PmBBM. Expression profiling analysis revealed the dynamic expression patterns of PmBBM and AP2 transcription factor family members during somatic embryogenesis. This study established the first reference-quality transcriptome database for P. mongolica using PacBio long-read sequencing, providing essential genomic resources for non-model species that lack a reference genome. Our findings not only advance the understanding of the molecular mechanisms underlying somatic embryogenesis, but also lay a solid foundation for future functional genomics research, including key gene validation and molecular marker-assisted breeding programs. These results have important theoretical and practical implications for the conservation and sustainable utilization of this endangered conifer species.