Analysis of the transcriptome of<i>Isodon rubescens</i>and key enzymes involved in terpenoid biosynthesis

Su, Xiuhong; Li, Qinglei; Chen, Suiqing; Dong, Chengming; Hu, Yuansen; Yin, Lei; Yang, Jian

doi:10.1080/13102818.2016.1146086

Cited by 14 publications

(9 citation statements)

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“…This indicates the good de novo assembly of the I. amethystoides transcriptomic data. In its relative species Isodon reubescens , Su et al [ 6 ] generated a dataset of 44,626 unigenes from leaf transcriptome, and 57.54% (25677) were annotated in one of the databases. In this study, we obtained more unigenes (approximately three folds) in I. amethystoides by comparative analysis of root, stem and leaves, which provide more abundant genetic information for understanding the molecular mechanism of Wangzoazins biosynthesis.…”

Section: Discussionmentioning

confidence: 99%

“…There are approximately 150 species of Isodon , nearly 70% of which are distributed in tropical and subtropical Asia [ 1 , 2 ]. Many Isodon species have been shown to be effective in treating different illness, including I. japonicus for bleomycin-induced pulmonary fibrosis [ 3 ], I. eriocalyx for autoimmune encephalomyelitis amelioration [ 4 ], I. phyllostachys for its antiphlogistic and antibiotic actions [ 5 ], and I. rubescens for its anticancer, anti-inflammatory, and antibacterial properties [ 6 ]. Isodon amethystoides (Ben-th) Cy Wu et Hsuan, referred to as “Wang Zao Zi” and “Xiang Cha Cai” in China, is known for its broad applications as a folk remedy for abscesses, swollen sores, and tumors [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

“…For non-sequenced medicinal plants, RNA-seq provides an efficient tool for us to generate large amount of omics data. For Isodon species, the transcriptomic data were reported in I. rubescens [ 6 , 21 ], but it has not been recorded in I. amethystoides and other species yet. In the present study, we report transcriptome databases from the root, stem, and leaf tissues of one-year-old I. amethystoides plants.…”

Section: Introductionmentioning

confidence: 99%

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Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

et al. 2018

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BackgroundIsodon amethystoides (Ben-th) Cy Wu et Hsuan is an important traditional medicinal plant endowed with pharmacological properties effective in the treatment of various diseases, including pulmonary tuberculosis. The tetracyclic diterpenoids, Wangzaozins (Wangzaozin A, glaucocalyxin A, glaucocalyxin B), are the major bioactive compounds of I. amethystoides. However, the molecular information about the biosynthesis of these compounds still remains unclear.ResultsAn examination of the accumulated levels of Wangzaozins in I. amethystoides revealed considerable variations in the root, stem, and leaf tissues of this plant, indicating possible differences in metabolite biosynthesis and accumulation among various tissues. To better elucidate the tetracyclic diterpenoid biosynthesis pathway, we generated transcriptome sequences from the root, stem, and leaf tissues, and performed de novo sequence assembly, yielding 230,974 transcripts and 114,488 unigenes, with average N50 lengths of 1914 and 1241 bp, respectively. Putative functions could be assigned to 73,693 transcripts (31.9%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. Moreover, the candidate genes involving in the diterpenoid biosynthesis, such as CPS, KSL, were also analyzed. The expression profiles of eight transcripts, involving the tetracyclic diterpenoid biosynthesis, were validated in different I. amethystoides tissues by qRT-PCR, unraveling the gene expression profile of the pathway. The differential expressions of ISPD, ISPF and ISPH (MEP pathway), and IaCPS and IaKSL (diterpenoid pathway) candidate genes in leaves and roots, may contribute to the high accumulation of Wangzaozins in I. amethystoides leaves.ConclusionThe genomic dataset and analyses reported here lay the foundations for further research on this important medicinal plant.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1505-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

et al. 2018

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“…Complementary deoxyribonucleic acid (cDNA) library construction, sequencing, and assembly were performed following the methods of Su [ 31 ], Ma [ 32 ] and Wang [ 33 ]. Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA), and index codes were added to attribute sequences to each sample.…”

Section: Methodsmentioning

confidence: 99%

Physiological and de novo transcriptome analysis of the fermentation mechanism of Cerasus sachalinensis roots in response to short-term waterlogging

et al. 2017

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Background Cerasus sachalinensis is widely used in cool regions as a sweet cherry rootstock and is known for its sensitivity to soil waterlogging and waterlogging stress. However, the limited availability of Cerasus genomic resources has considerably restricted the exploration of its waterlogging response mechanism. To understand its reaction to short-term waterlogging, we analyzed the physiology and transcriptomes of C. sachalinensis roots in response to different waterlogging durations.ResultsIn this study, 12,487 differentially expressed genes (DEGs) were identified from Cerasus sachalinensis roots under different waterlogging durations. Carbon metabolism and energy maintenance formed the first coping mechanism stage of C. sachalinensis in response to low oxygen conditions. Root energy processes, including root respiration and activities of the fermentation enzymes alcohol dehydrogenase, pyruvate decarboxylase, and lactate dehydrogenase, showed unique changes after 0 h, 3 h, 6 h, and 24 h of waterlogging exposure. Ribonucleic acid sequencing was used to analyze transcriptome changes in C. sachalinensis roots treated with 3 h, 6 h, and 24 h of waterlogging stress. After de novo assembly, 597,474 unigenes were recognized, of which 355,350 (59.47%) were annotated. To identify the most important pathways represented by DEGs, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to compare these genes. The first stage of root reaction to waterlogging stress was activation of carbohydrate metabolism to produce more glucose and maintain energy levels. At 3 h, the glycolytic and fermentation pathways were activated to maintain adenosine triphosphate production. At 24 h, pathways involved in the translation of proteins were activated to further assist the plant in tolerating waterlogging stress. These findings will facilitate a further understanding of the potential mechanisms of plant responses to waterlogging at physiological and transcriptome levels.ConclusionsCarbon metabolism and energy maintenance formed the first coping mechanism C. sachalinensis in response to low oxygen conditions, and they may be responsible for its short-term waterlogging response. Our study not only provides the assessment of genomic resources of Cerasus but also paves the way for probing the metabolic and molecular mechanisms underlying the short-term waterlogging response in C. sachalinensis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4055-1) contains supplementary material, which is available to authorized users.

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“…4 ). The gene for aldehyde oxidase 3 ( NiAAO3 ) catalyzed the last step of ABA biosynthesis [ 29 ] was down-regulated (~ 2.1-fold) in FL (Fig. 4 , Additional file 10 : Table S3).…”

Section: Resultsmentioning

confidence: 99%

Molecular mechanism of seed dormancy release induced by fluridone compared with cod stratification in Notopterygium incisum

Li¹,

Jiang²,

Guang³

et al. 2018

BMC Plant Biol

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BackgroundNotopterygium incisum is an important Chinese medicinal plant. Its mature seeds have underdeveloped embryos and are physiological dormant. We found the seeds with full developed embryos can germinate after treated by fluridone (FL), an inhibitor of abscisic acid (ABA). In order to understand the molecular mechanisms underlying seed dormancy release by FL, we compared the transcriptomic changes in dormancy release induced by two different methods, FL and cold stratification (CS) in N. incisum. We further analyzed the gene expression patterns involved in seed germination and dormancy using quantitative reverse-transcription PCR.ResultsRNA-sequence analysis revealed more dramatic changes in the transcriptomes of FL than those in CS, particularly for genes involved in the biosynthesis and regulation of gibberellins (GAs) and ABA. The down-regulation of ABA biosynthesis genes and the dramatic up-regulation of NiCYP707As, an ABA catabolic gene, contributed to the reduced ABA levels in FL. The increased GA3 levels in CS-treated seeds were due to the up-regulation of NiGA3OX. Both NiABI5 (a positive ABA regulator) and NiGAI (a negative regulator of GA) were down-regulated in FL and CS. The upregulation of strigolactones (SLs; the metabolites with the same precursor as ABA) biosynthesis and regulatory genes in both FL- and CS-treated seeds indicates that SLs contribute positively to seed dormancy release in N. incisum.ConclusionsOur results indicated that FL- and CS-seed dormancy release possibly depends on two totally different mechanisms: alleviation of the effects of ABA and potentiation of the effects of GA, respectively. However, NiABI5 and NiGAI probably function as common factors integrating the effects of ABA and GA on seed dormancy release.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1333-2) contains supplementary material, which is available to authorized users.

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Analysis of the transcriptome ofIsodon rubescensand key enzymes involved in terpenoid biosynthesis

Cited by 14 publications

References 30 publications

Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

Physiological and de novo transcriptome analysis of the fermentation mechanism of Cerasus sachalinensis roots in response to short-term waterlogging

Molecular mechanism of seed dormancy release induced by fluridone compared with cod stratification in Notopterygium incisum

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