Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of <i>Gnetum</i> (Gnetales)

The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. <i>Gnetum</i>, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of <i>Gnetum luofuense</i> leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the <i>G. luofuense</i> leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the <i>bHLH</i> gene family, which play an important role in stomatal development and photosynthesis, were identified from the <i>G. luofuense</i> genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of <i>G. luofuense</i>, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of <i>Gnetum</i>.