Reverse Transcription-PCR analysis of geranylgeranyl diphosphate synthase (JcGGPPS) in Jatropha curcas L. and in silico analysis of Casbene Synthase (JcCS) among Euphorbiaceae

Jadid, Nurul; Mardika, Rizal Kharisma; Nurhidayati, Tutik; Irawan, Mohammad Isa

doi:10.1063/1.4953516

Cited by 10 publications

(5 citation statements)

References 25 publications

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“…The samples used for gDNA extraction were obtained from 150 mg of R trisperma leaves, which were ground using liquid nitrogen prior to extraction. 45 Meanwhile, we used Plant Total RNA Mini Kit (Genaid) to isolate the total RNA from R trisperma seeds, as described by Jadid et al 46 The plant endosperm was prepared and ground in liquid nitrogen. We measured the concentration and quality of the DNA and total RNA extracts using NanoDrop ™ .…”

Section: Methodsmentioning

confidence: 99%

Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production

Jadid,

Rosidah,

Ramadani

et al. 2023

Bioinform Biol Insights

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Reutealis trisperma belonging to the family Euphorbiaceae is currently used for biodiesel production, and rapid development in plant-based biofuel production has led to its increasing demand. However, massive utilization of bio-industrial plants has led to conservation issues. Moreover, genetic information on R trisperma is still limited, which is crucial for developmental, physiological, and molecular studies. Studying gene expression is essential to explain plant physiological processes. Nonetheless, this technique requires sensitive and precise measurement of messenger RNA (mRNA). In addition, the presence of internal control genes is important to avoid bias. Therefore, collecting and preserving genetic data for R trisperma is indispensable. In this study, we aimed to evaluate the application of plastid loci, rbcL, and matK, to the DNA barcode of R trisperma for use in conservation programs. In addition, we isolated and cloned the RtActin ( RtACT) gene fragment for use in gene expression studies. Sequence information was analyzed in silico by comparison with other Euphorbiaceae plants. For actin fragment isolation, reverse-transcription polymerase chain reaction was used. Molecular cloning of RtActin was performed using the pTA2 plasmid before sequencing. We successfully isolated and cloned 592 and 840 bp of RtrbcL and RtmatK fragment genes, respectively. The RtrbcL barcoding marker, rather than the RtmatK plastidial marker, provided discriminative molecular phylogenetic data for R Trisperma. We also isolated 986 bp of RtACT gene fragments. Our phylogenetic analysis demonstrated that R trisperma is closely related to the Vernicia fordii Actin gene (97% identity). Our results suggest that RtrbcL could be further developed and used as a barcoding marker for R trisperma. Moreover, the RtACT gene could be further investigated for use in gene expression studies of plant.

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Section: Methodsmentioning

confidence: 99%

Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production

Jadid,

Rosidah,

Ramadani

et al. 2023

Bioinform Biol Insights

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“…Tomato leaves of each genotype were subjected to total gDNA extraction as described previously. 28 The extraction was performed using “Plant Genomic DNA Mini Kit” (Geneaid®, Taiwan) according to the kit’s instructions. Measurement of gDNA quantity and quality was conducted using “Nano Drop” (Thermo Scientific™ nanodrop 2000).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and growth responses of Indonesian tomato (Solanum lycopersicum L.) genotypes under lead stress

et al. 2022

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Tomato ( Solanum lycopersicum L.) is cultivated and consumed worldwide, including in Indonesia. It is used in the food, cosmetic, and pharmaceutical industries, due to its high content of carotenoid (lycopene) compounds that have antioxidant and anticancer activities. In Indonesia, although several cultivars of tomato are cultivated, including Opal, Permata, Mutiara, and Rewako , studies on their genetic information are limited. Unpredicted climate change as well as heavy metal contamination, especially Pb pollution, has threatened Indonesian food security. Therefore, our study aimed to analyze the genetic diversity of the four local tomatoes using random amplified polymorphic DNA (RAPD) markers and to determine the growth responses of several local tomato genotypes under Pb stress. In this study, morphological responses to Pb, including plant height and root length were observed. The RAPD analysis showed that Rewako and Permata were distinct, whereas Opal and Mutiara were closely related, possessing 81.8% similarity. Pb stress influenced plant height and root length in the four tomato genotypes, with each genotype exhibiting different morphological responses than others. However, the closely related Mutiara and Opal genotypes demonstrated similar responses to Pb stress to Permata and Rewako. Our study demonstrates that RAPD are sensitive and efficient for elucidating the genomic profile of the tomato genotypes. In addition, our results suggest that genetic variation among tomato genotypes might influence the morphological responses against Pb stress.

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“…Total RNA extraction was carried out using the Plant Total RNA Mini Kit (Genaid) according to Jadid et al 24 The seeds were peeled, and the endosperm was thinly dissected and immediately placed into a 1.5-mL tube floating on liquid nitrogen. Total RNA concentration was quantified using a Nanodrop spectrophotometer (ND-1000, Thermo Scientific, USA).…”

Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Partial Fatty Acid Desaturase 2 cDNA From Reutealis trisperma (Blanco) Airy Shaw

Jadid

Prasetyowati

Rosidah

et al. 2021

Bioinform Biol Insights

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Reutealis trisperma oil is a new source for biodiesel production. The predominant fatty acids in this plant are stearic acid (9%), palmitic acid (10%), oleic acid (12%), linoleic acid (19%), and α-eleostearic acid (51%). The presence of polyunsaturated fatty acids (PUFAs), linoleic acid, and α-eleostearic acid decreases the oxidation stability of R. trisperma biodiesel. Although several studies have suggested that the fatty acid desaturase 2 (FAD2) enzyme is involved in the regulation of fatty acid desaturation, little is known about the genetic information of FAD2 in R. trisperma. The objectives of this study were to isolate, characterize, and determine the relationship between the R. trisperma FAD2 fragment and other Euphorbiaceae plants. cDNA fragments were isolated using reverse transcription polymerase chain reaction (PCR). The DNA sequence obtained by sequencing was used for further analysis. In silico analysis identified the fragment identity, subcellular localization, and phylogenetic construction of the R. trisperma FAD2 cDNA fragment and Euphorbiaceae. The results showed that a 923-bp partial sequence of R. trisperma FAD2 was successfully isolated. Based on in silico analysis, FAD2 was predicted to encode 260 amino acids, had a domain similarity with Omega-6 fatty acid desaturase, and was located in the endoplasmic reticulum membrane. The R. trisperma FAD2 fragment was more closely related to Vernicia fordii (HM755946.1).

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Reverse Transcription-PCR analysis of geranylgeranyl diphosphate synthase (JcGGPPS) in Jatropha curcas L. and in silico analysis of Casbene Synthase (JcCS) among Euphorbiaceae

Cited by 10 publications

References 25 publications

Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production

Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production

Genetic diversity and growth responses of Indonesian tomato (Solanum lycopersicum L.) genotypes under lead stress

In Silico Analysis of Partial Fatty Acid Desaturase 2 cDNA From Reutealis trisperma (Blanco) Airy Shaw

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