Dataset Information

Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales.

ABSTRACT: The Lamiales order presents highly varied genome sizes and highly specialized life strategies. Patchouli, Pogostemon cablin (Blanco) Benth. from the Lamiales, has been widely cultivated in tropical and subtropical areas of Asia owing to high demand for its essential oil. Here, we generated ~681?Gb genomic sequences (~355X coverage) for the patchouli, and the assembled genome is ~1.91?Gb and with 110,850 predicted protein-coding genes. Analyses showed clear evidence of whole-genome octuplication (WGO) since the pan-eudicots ? triplication, which is a recent and exclusive polyploidization event and occurred at ~6.31 million years ago. Analyses of TPS gene family showed the expansion of type-a, which is responsible for the synthesis of sesquiterpenes and maybe highly specialization in patchouli. Our datasets provide valuable resources for plant genome evolution, and for identifying of genes related to secondary metabolites and their gene expression regulation.

SUBMITTER: He Y

PROVIDER: S-EPMC6289116 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales.

He Yang Y Peng Fu F Deng Cao C Xiong Liang L Huang Zi-Yan ZY Zhang Ruo-Qi RQ Liu Meng-Jia MJ Peng Cheng C

Scientific data 20181211

The Lamiales order presents highly varied genome sizes and highly specialized life strategies. Patchouli, Pogostemon cablin (Blanco) Benth. from the Lamiales, has been widely cultivated in tropical and subtropical areas of Asia owing to high demand for its essential oil. Here, we generated ~681 Gb genomic sequences (~355X coverage) for the patchouli, and the assembled genome is ~1.91 Gb and with 110,850 predicted protein-coding genes. Analyses showed clear evidence of whole-genome octuplication ...[more]

PMID: 30532075

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Project description:Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type "Nanxiang" (NX) and PO-type "Paixiang" (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

Dataset Information

Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales.

Publications

Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales.

Similar Datasets

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