LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive. For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding. We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.

中文翻译：

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综合lncRNA景观揭示了毛竹次生细胞壁生物合成途径中的lncRNA编码基因网络（Phyllostachys edulis）

LncRNA 广泛参与植物生物学过程。然而，毛竹中缺乏全面的lncRNA景观阻碍了lncRNA的分子研究。此外，lncRNA在毛竹次生细胞壁（SCW）生物合成中的作用尚不清楚。为了全面识别整个毛竹基因组中的 lncRNA，我们收集了 231 个 RNA-Seq 数据集、1 个 Iso-Seq 数据集和 1 个全长 cDNA 数据集。我们在以往研究的基础上，使用机器学习方法改进了 lncRNA 识别和功能注释的流程，并在毛竹中识别了 37,009 个 lncRNA。然后，我们建立了一个用于 SCW 生物合成的潜在 lncRNA 编码基因网络，并确定了 SCW 相关的 lncRNA。我们还提出竹子中存在一种机制，通过 PAL/4CL/C4H 基因将苯丙素中间体引导至木质素或类黄酮生物合成。此外，我们在 PAL/4CL/C4H 基因家族中鉴定了 4 个类黄酮和 1 个木质素偏好基因，这对分子育种具有重要意义。我们提供了毛竹中 lncRNA 的综合概况。通过分析，我们确定了 SCW 相关的 lncRNA，并提高了我们对木质素和类黄酮生物合成的理解。