Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio’s SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA’s role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.

中文翻译：

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降香黄檀木材形成相关转录后过程的全基因组表征

选择性多腺苷酸化 (APA)、选择性剪接 (AS) 和长链非编码 RNA (lncRNA) 在植物转录后过程中发挥调节作用。然而，人们对它们在降香黄檀木质部发育中的参与知之甚少，降香黄檀是一种具有药用和商业意义的珍贵红木树种。我们通过使用 PacBio 的 SMRT 技术进行异构体测序 (Iso-Seq) 来解决这个问题，并在从 D. odorifera 的过渡区和边材收集木质部样本后将其与 RNA-seq 分析（在 Illumina 平台上进行 RNA 测序）相结合。我们鉴定了 14,938 个全长转录本，包括 9,830 个新亚型，更新了 D. odorifera 基因组注释。我们的分析表明，4,164 个基因经历 APA，而 3,084 个基因经历 AS。我们还注释了 118 个 lncRNA。此外，RNA-seq 分析确定了过渡区与边材相比的 170 个差异选择性剪接 (DAS) 事件、344 个具有差异 APA 位点使用 (DE-APA) 的基因以及 6 个差异表达的 lncRNA。 AS、APA 和 lncRNA 在木质部发育过程中受到不同的调控。差异表达的 APA 基因在萜类化合物和类黄酮代谢中富集，表明它们在心材形成中的作用。此外，DE-APA 基因与细胞壁生物合成和萜类化合物代谢相关，这意味着 APA 在木材形成中的作用。鉴定出一个 DAS 基因（参与查尔酮积累），其最后一个外显子在过渡区的含量显着高于边材。我们还发现差异表达的lncRNA靶向与萜烯合成相关的基因。这项研究增强了我们对香木木材形成分子调控机制的理解，并为其分子辅助育种提供了宝贵的遗传资源和见解。