De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L

2021 ◽  
pp. 1-8
Author(s):  
Tanuja ◽  
Nibir Ranjan Parasar ◽  
Ravichandiran Kumar ◽  
Purushothaman Natarajan ◽  
Madasamy Parani
Keyword(s):  
Transcription Factors ◽  
De Novo ◽  
Phenylpropanoid Pathway ◽  
Medicinal Species ◽  
Ocimum Gratissimum ◽  
Leaf Transcriptome ◽  
Molecular Studies ◽  
Molecular Phylogenetic ◽  
Caffeine Biosynthesis ◽  
Caffeine Metabolism

Abstract Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Enhanced accumulation of pinosylvin stilbenes and related gene expression in Pinus strobus after infection of pine wood nematode

2021 ◽  
Author(s):  
Hwan-Su Hwang ◽  
Jung Yeon Han ◽  
Yong Eui Choi
Keyword(s):  
Transcription Factors ◽  
Defense Mechanisms ◽  
De Novo ◽  
Pinus Strobus ◽  
Pine Wilt Disease ◽  
Monomethyl Ether ◽  
Bursaphelenchus Xylophilus ◽  
Nematicidal Activity ◽  
Dependent Manner ◽  
Pine Wood

Abstract Pine wood nematodes (PWNs: Bursaphelenchus xylophilus) infect pine trees and cause serious pine wilt disease. Eastern white pine (Pinus strobus) has resistance to PWN. However, the detailed defense mechanisms of P. strobus against PWN are not well known. When P. strobus plants were infected with PWNs, the accumulation of stilbenoids, dihydropinosylvin monomethyl ether (DPME) and pinosylvin monomethyl ether (PME), were increased remarkably. DPME and PME had the high nematicidal activity. Interestingly, the nematicidal activity of the two compounds was resulted in a developmental stage-dependent manner. PME was more toxic to adult PWNs than juveniles, whereas DPME was found more toxic to juvenile PWNs than the adults. The genes involved in PME and DPME biosynthesis such as phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), pinosylvin synthase (STS), and pinosylvin O-methyltransferase (PMT) were isolated using de novo sequencing of the transcriptome in P. strobus. In addition, transcription factors (bHLH, MYB and WRKY) related to stilbene biosynthesis were isolated. qPCR analyses of the selected genes (PAL, 4CL, STS, and PMT) including transcription factors (bHLH, MYB and WRKY) revealed that the expression level of the selected genes highly enhanced after PWN infection. Our results suggest that pinosylvin-type stilbenoid biosynthesis is highly responsive to PWN infection and plays an important role in PWN resistance of P. strobus trees.

scholarly journals Salivary caffeine in Parkinson’s disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giorgio Leodori ◽  
Maria Ilenia De Bartolo ◽  
Daniele Belvisi ◽  
Alessia Ciogli ◽  
Andrea Fabbrini ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Rating Scale ◽  
De Novo ◽  
Oral Intake ◽  
Caffeine Intake ◽  
Motor Complications ◽  
Disease Rating ◽  
Caffeine Metabolism ◽  
Movement Disorder Society

AbstractWe aimed to investigate salivary caffeine content, caffeine absorption and metabolism in Parkinson’s disease (PD) and verify whether salivary caffeine can be used as a biomarker of PD. We enrolled 98 PD patients and 92 healthy subjects. Caffeine and its major metabolite, paraxanthine, were measured in saliva samples collected before and 4 h after the oral intake of caffeine (100 mg). We measured caffeine absorption as the normalized increase in caffeine levels, and caffeine metabolism as the paraxanthine/caffeine ratio. The Movement Disorder Society Unified Parkinson's Disease Rating Scale part III, the Hoehn & Yahr, the presence of motor complications, and levodopa equivalent dose (LED) were assessed and correlated with caffeine levels, absorption, and metabolism. The effects of demographic and environmental features possibly influencing caffeine levels were also investigated. Caffeine levels were decreased in patients with moderate/advanced PD, while caffeine levels were normal in patients with early and de-novo PD, unrelated to caffeine intake. Caffeine absorption and metabolism were normal in PD. Decreased salivary caffeine levels in PD were associated with higher disease severity, longer duration, and the presence of motor complications, no significant association was found with LED. Salivary caffeine decrease correlates with PD progression.

De novo leaf transcriptome of a triploid linalool chemotype of Lippia alba (Mill.) N.E.Br. ex Britton & P. Wilson

2021 ◽  
Author(s):  
V. C. de Souza ◽  
M. M. Aragão ◽  
L. S. Tavares ◽  
P. V. S. Z. Capriles ◽  
L. F. Viccini ◽  
...  
Keyword(s):  
De Novo ◽  
Lippia Alba ◽  
Leaf Transcriptome

scholarly journals Elucidating genes involved in sesquiterpenoid and flavonoid biosynthetic pathways in Saussurea lappa by de novo leaf transcriptome analysis

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1474-1482 ◽  
Author(s):  
Savita Bains ◽  
Vasundhara Thakur ◽  
Jagdeep Kaur ◽  
Kashmir Singh ◽  
Ravneet Kaur
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Saussurea Lappa ◽  
Leaf Transcriptome

Caffeine Metabolism in High and Low Caffeine Containing Cultivars of Camellia sinensis

1995 ◽  
Vol 50 (9-10) ◽  
pp. 602-607 ◽  
Author(s):  
Hiroshi Ashihara ◽  
Hisayo Shimizu ◽  
Yoshiyuki Takeda ◽  
Takeo Suzuki ◽  
Fiona M. Gillies ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Adenine Nucleotides ◽  
Vitro Activity ◽  
Biosynthesis Pathway ◽  
Rapid Rate ◽  
In Vitro Activity ◽  
Caffeine Content ◽  
Caffeine Biosynthesis ◽  
Caffeine Metabolism

Abstract The metabolism of [8-14C ]adenine and [2-14C]caffeine was examined in leaf segments from flush shoots of tea cultivars with high and low caffeine content. The caffeine biosynthesis pathway from AMP via theobromine was operative in both high and low caffeine containing cultivars. There was a m ore rapid rate of caffeine biosynthesis from [8-14C ]adenine in the high caffeine cultivars while the rate of degradation of both adenine nucleotides and caffeine into CO2 was greatest in cultivars with a low endogenous caffeine content. Cell-free p reparations from tea shoots contained an N-methyltransferase, that is a keyenzyme in the caffeine biosynthesis pathway; more in-vitro activity was detected in preparations from high caffeine containing cultivars. The data obtained suggest that the high caffeine containing cultivars have a more rapid rate of caffeine biosynthesis and a slower rate of caffeine catabolism than cultivars with a low endogenous caffeine content

A dual role for the protein kinase shaggy in the repression of achaete­scute

Development ◽  
1993 ◽  
Vol 119 (Supplement) ◽  
pp. 29-39 ◽  
Author(s):  
Pat Simpson ◽  
Laurent Ruel ◽  
Pascal Heitzler ◽  
Marc Bourouis
Keyword(s):  
Transcription Factors ◽  
Protein Kinase ◽  
Glycogen Synthase ◽  
Precursor Cell ◽  
The Other ◽  
Glycogen Synthase Kinase 3 ◽  
Neural Precursor ◽  
Constitutive Activity ◽  
Molecular Studies ◽  
Restricted Pattern

achaete and scute are expressed in a spatially restricted pattern and provide neural potential to cells. The domains of expression depend partly on extramacrochaetae whose product is itself spatially restricted and acts as a negative post-translational regulator of achaete and scute. The protein kinase shaggy also represses achaete and scute at many sites but may act via intermediate transcription factors. However shaggy and exlramacrochaetae act synergistically and molecular studies suggest that they may be part of the same pathway, shaggy is functionally homologous to the mammalian glycogen synthase kinase-3 and analogy with the known physiology of this enzyme, suggests that this function of shaggy may result from the “constitutive” activity. At the site where a single neural precursor will develop, achaete and scute are initially expressed in a group of equivalent cells. The genes Notch and Delta are part of a lateral signal required to single out one precursor cell and to silence achaete and scute expression in the other cells, shaggy is required downstream of Notch for transduction of the inhibitory signal. This second role or shaggy may be due to modulation or enzymatic activity during signalling.

scholarly journals De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Nitesh Kumar Sharma ◽  
Pooja Thapa ◽  
Isha Sharma ◽  
Mohit Kumar Swarnkar ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
De Novo ◽  
Natural Habitat ◽  
Sugar Metabolism ◽  
Western Himalaya ◽  
Metabolite Profile ◽  
Clonal Plants ◽  
Phenylpropanoid Pathway ◽  
Terrestrial Orchid ◽  
Metabolite Synthesis

Abstract This is the first report on de novo transcriptome of Dactylorhiza hatagirea, a critically-endangered, terrestrial orchid of alpine Himalayas. The plant is acclaimed for medicinal properties but little is known about its secondary-metabolites profile or cues regulating their biosynthesis. De novo transcriptome analysis was therefore, undertaken to gain basic understanding on these aspects, while circumventing the acute limitation of plant material availability. 65,384 transcripts and finally, 37,371 unigenes were assembled de novo from a total of 236 million reads obtained from shoot, tuber and leaves of the plant. Dominance of differentially-expressing-genes (DEGs) related to cold-stress-response and plant-hormone-signal-transduction; and those involved in photosynthesis, sugar-metabolism and secondary-metabolite-synthesis provided insights into carbohydrate-partitioning in the plant during its preparation for freezing winter at natural habitat. DEGs of glucomannan, ascorbic acid, carotenoids, phylloquinone/naphthoquinones, indole alkaloids, resveratrol and stilbene biosynthesis revealed the secondary-metabolite profile of D. hatagirea. UHPLC results confirmed appreciable amounts of resveratrol and trans-stilbene in D. hatagirea tubers, for the first time. Expression analysis of 15 selected genes including those of phenylpropanoid pathway confirmed the validity of RNA-seq data. Opportunistic growth, temperature- and tissue-specific-differential-expression of secondary metabolite biosynthesis and stress tolerant genes were confirmed using clonal plants growing at 8, 15 and 25 °C.

scholarly journals Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nithiwat Suntichaikamolkul ◽  
Kittitya Tantisuwanichkul ◽  
Pinidphon Prombutara ◽  
Khwanlada Kobtrakul ◽  
Julie Zumsteg ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Biosynthetic Genes ◽  
Pueraria Candollei ◽  
Isoflavone Synthase ◽  
Young Leaves ◽  
Plausible Mechanism ◽  
Polymerase Chain ◽  
R2r3 Myb

Abstract Background Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown. Results Miroestrol biosynthesis was reconsidered and the most plausible mechanism starting from the isoflavonoid daidzein was proposed. A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers. A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidates involved in these biosynthetic pathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid and miroestrol profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica. To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor (AtMYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins led to the production of the isoflavone genistein. Conclusions Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for identifying biosynthetic genes and transcription factors possibly involved in the isoflavonoid and miroestrol biosyntheses in P. candollei var. mirifica.

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