Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Tsai, Ching‐Chih; Wu, Keh Ming; Chiang, Tzen‐Yuh; Huang, Chengfei; Chou, Chih-Hsing; Li, Shu Ju; Chiang, Yu Chung

doi:10.1186/s12864-016-2508-6

Cited by 45 publications

(47 citation statements)

References 84 publications

(81 reference statements)

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“…RNA-illumina sequencing technology has been extensively used for identifying gene expression at a genome-wide scale in many organisms, including non-model plants. The adoption of this technique, especially mRNA sequencing from floral tissues and de novo transcriptome construction (Figure 4), has been performed in several orchid species, with a goal of identifying genes involved in the biosynthesis and/or biosynthetic pathways of floral volatiles [28,110]. Moreover, other strategies include molecular evolutionary analysis tools.…”

Section: Final Remarks and Future Directions For Overcome The Challengesmentioning

confidence: 99%

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Ramya¹,

Jang²,

An³

et al. 2020

IJMS

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Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.

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Section: Final Remarks and Future Directions For Overcome The Challengesmentioning

confidence: 99%

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Ramya¹,

Jang²,

An³

et al. 2020

IJMS

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“…For further development and enlargement of tubers, flowering and fruit setting, Armillaria becomes essential for the nutrient supply. It is also noteworthy that G. elata is a well-known Chinese medicinal orchid (Tsai et al 2016). Recently, a number of pharmacological experiments indicated that it had strong potential to combat Alzheimer’s disease, Parkinson’s disease and other neurodegenerative diseases (Manavalan et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata

Ling

et al. 2017

Bot Stud

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Background Gastrodia elata is a well-known medicinal orchid. In nature, the germination rate of G. elata is extremely poor, because there is no endosperm within the mature seed. It is crucial for G. elata to obtain nutrition from mycorrhizal fungi (Mycena) at the early-stage of germination. After germination, the seed gives rise to a protocorm. However, there are no “omic” studies on understanding the interaction between Gastrodia and Mycena. Here, we used transcriptomic approaches to explore changes in seed germination of G. elata.ResultsBased on RNA-Seq, a total of ~221 million clean reads were assembled denovo into 139,756 unigenes, including 42,140 unigenes that were annotated in public databases. Meanwhile, 1750 unigenes were identified as differentially expressed genes. Most of these differentially expressed genes were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Additionally, numerous genes involved in clathrin-mediated endocytosis were identified from our data. Most of these genes (e.g., clathrin, adaptor protein, dynamin, HSC70) were basally expressed in seeds and highly expressed in protocorms.ConclusionsOur data suggested that clathrin-mediated endocytosis could play important roles in symbiotic seed germination of G. elata with Mycena infections.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-017-0185-7) contains supplementary material, which is available to authorized users.

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“…Furthermore, "membrane part" (15,180 unigenes [43.72%]) and "cell" (12,907 unigenes [37.18%]) were the most enriched GO terms within the "cellular component" category; A total of 80,140, 79,085, 96,382, and 73,919 unigenes were counted in the RNA-Seq data sets of flower, leaf, stem, and root tissues, of which 10,888, 8128, 7145 and 9085 unigenes with FPKM ≥10 showed high expression, 27,832, 26,890, 26,903 and 21,844 unigenes with FPKM = 1-10 showed medium expression, and 41,420, 44,067, 62,334 and 42,950 unigenes with FPKM ≤1 showed low expression, respectively ( Fig. 3a) [25,26]. The overall expression level of unigenes was the highest in flowers, followed by stems, leaves, and roots ( Fig.…”

Section: Functional Classification and Expressed Overview Of Unigenesmentioning

confidence: 99%

Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis

et al. 2020

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Background: Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bioactive compounds in C. gracile. However, the molecular understanding of the triterpenoid saponin biosynthesis pathway remains unclear. Results: In this study, we performed RNA sequencing (RNA-Seq) analysis of the flowers, leaves, roots, and stems of C. gracile plants using the BGISEQ-500 platform. The assembly of transcripts from all four types of tissues generated 128,856 unigenes, of which 99,020 were mapped to several public databases for functional annotation. Differentially expressed genes (DEGs) were identified via the comparison of gene expression levels between leaves and other tissues (flowers, roots, and stems). Multiple genes encoding pivotal enzymes, such as squalene synthase (SS), or transcription factors (TFs) related to triterpenoid saponin biosynthesis were identified and further analyzed. The expression levels of unigenes encoding important enzymes were verified by quantitative real-time PCR (qRT-PCR). Different chemical constituents of triterpenoid saponins were identified by Ultra-Performance Liquid Chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Conclusions: Our results greatly extend the public transcriptome dataset of C. gracile and provide valuable information for the identification of candidate genes involved in the biosynthesis of triterpenoid saponins and other important secondary metabolites.

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Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Cited by 45 publications

References 84 publications

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata

Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis

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