Zhang Hongyi, Deng Wenjing, Lu Changhua, He Mengling, Yan Hanjing
College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.
PeerJ. 2022 Feb 22;10:e12940. doi: 10.7717/peerj.12940. eCollection 2022.
(Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil.
To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads.
In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of . We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were "terpenoid backbone biosynthesis", "phenylpropanoid biosynthesis", "plant hormone signal transduction", "sesquiterpenoid and triterpenoid biosynthesis", "ubiquinone and other terpenoid-quinone biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". However, the main pathways of the patchouliol-type also included "diterpene biosynthesis" and "monoterpene biosynthesis". Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in .
广藿香（Blanco）Benth.，也叫藿香，是一种传统的药用和芳香植物，主要生长在东南亚和中国。在中国，广藿香分为两种化学类型：广藿香醇型和百秋李醇型。广藿香醇型广藿香通常长得更高，茎更粗，叶子更大，并且产生更多的芳香油。
为了更好地理解导致两种化学类型在形态和生物合成能力上存在差异的遗传差异，我们使用太平洋生物科学公司（PacBio）的Sequel平台构建了两种化学类型的转录组，并使用Illumina短读长对多个组织进行了差异表达分析。
在本研究中，我们使用单分子实时（SMRT）长读长测序，从两种化学类型中获得了22.07GB的clean数据和134,647条非冗余转录本。此外，我们从两种化学类型的广藿香中鉴定出126,576个开放阅读框（ORF）、100,638个编码序列（CDS）、4,106个长链非编码RNA（lncRNA）和6,829个转录因子（TF）。我们采用PacBio和Illumina测序来鉴定两种化学类型的三个组织中的差异表达转录本（DEG）。相对于从不同化学类型收集的相同组织的比较，在从相同化学类型收集的不同组织的比较中观察到更多的DEG。此外，通过对DEG进行KEGG富集分析，我们发现两种化学类型的次生代谢物最富集的生物合成途径是“萜类骨架生物合成”、“苯丙烷类生物合成”、“植物激素信号转导”、“倍半萜和三萜生物合成”、“泛醌和其他萜类醌生物合成”、“类黄酮生物合成”以及“黄酮和黄酮醇生物合成”。然而，广藿香醇型的主要途径还包括“二萜生物合成”和“单萜生物合成”。此外，通过比较经qRT-PCR验证的三个组织的表达水平，根中更多的DEG在细胞质中的甲羟戊酸（MVA）途径中上调，但叶中更多的DEG在质体中的甲基赤藓糖醇磷酸（MEP）途径中上调，这两条途径都是萜类生物合成的重要途径。这些发现促进了广藿香进一步的基因组注释和转录组研究。
