22 research outputs found
Sesamum indicum Cytochrome P
No full text<i>4.11. Phylogenetic analysis of O. indicum cytochrome P 450</i> <p>Genes annotated as Cytochrome P 450 in the transcriptome were shortlisted (Supplementary Table 4). They were used to identify the full length ORFs of OinCyp450s with high FPKM values (above 5.5). Protein BLAST of the genes annotated as cytochrome P450 s was performed to identify the type /function of the specific Cytochrome P450. Phylogenetic tree of the newly identified, full length protein OinCyps was performed using MEGA7 by the maximum likelihood method (Kumar et al., 2016) (Fig. 5).</p> <p> <b>Conflicts of interest</b></p> <p>The authors declare no conflict of interest.</p> <p> <b>Acknowledgement</b></p> <p>The authors would like to acknowledge the Department of Biotechnology (DBT), Government of India for the DBT-BioCARE project to Dr. Vaijayanti Tamhane (BT/Bio-CARe/07/320/2012) and Departmental Research and Developmental Program (DRDP), Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India for funding this work. The authors are thankful to Ms. Meenakshi Kapse, Project Assistant, IBB, SPPU for helping with command line BLAST analysis of the transcriptome. The authors are grateful to Dr. Sneha Bansode, Department of Biotechnology, SPPU for her critical comments and suggestions. The transcriptome sequencing service was provided by Genotypic, Bangalore, India.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 211, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Oroxylum indicum subsp. root
No full text<i>2.1. Sequencing and De novo assembly of O. indicum root transcripts</i> <p> <i>De novo</i> transcriptome analysis is an excellent platform for generation of comprehensive information to deduce the basic biological, molecular and cellular processes for non-model organisms lacking whole genome sequences. To generate a transcriptome database for <i>O. indicum</i>, cDNA libraries of root tissue were sequenced using Illumina NextSeq 500. A total of 24,625,398 raw reads were generated comprising 3,718,435,098 nucleotides with an average size of 151 bp and 44% GC content (Table 1). Reads with Q <20 were removed. Reads were mapped to human reference transcriptome which showed absence of contamination of human transcripts. These high quality reads were used for <i>de novo</i> assembly using Trinity (Hass et al., 2013). It has been reported that the quality of a <i>de novo</i> assembly is dependent on many factors, such as the type of assembler used, followed by parameters like N50 value and coverage (Reddy et al., 2015). The data has been submitted to NCBI, Sequence Read Archive (SRA) submission: SUB2988844.</p> <p>The assembly resulted in a total of 121,286 transcripts with N50 value of 1783 bp with an average contig length of 1080 bp (Table 2). Furthermore, transcript clustering (CD-HIT-EST) resulted into 81,002 transcripts with an average contig length of 1071 bp and 1788 N50 value (Table 2). These 81,002 transcripts were further targeted for BLASTx analysis for functional annotation.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 202, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Oroxylum indicum subsp. root
No full text<i>2.6. Transcription factor analysis in the O. indicum root transcriptome</i> <p> At least six distinct transcription factors (TFs) namely myeloblastosis (MYB), basic helix-loop-helix (bHLH), WD or beta-transducin repeat (WD40), WRKY, Zinc finger and MADS box proteins are involved in flavonoid biosynthesis regulation (Terrier et al., 2009). Of these, three transcription factors MYB, bHLH and WD40 (MBW) were detected in the root transcriptome of <i>O. indicum</i> (Table 6; Supplementary Table 3). MYB11, MYB12 and MYB111 are known to control flavonol biosynthesis by activating the early biosynthetic steps (Nesi et al., 2002; Gou et al., 2011), while the MBW complex activates the late biosynthetic genes of flavonoid biosynthesis (Mehrtens et al., 2005; Stracke et al., 2007; Li, 2014). In the <i>O. indicum</i> root, the MYB transcription factor family was represented prominently, followed by WD40 and bHLH (Table 6; Supplementary Table 3). These transcription factors can either work individually or synergistically in controlling the multiple enzymatic steps involved in the flavonoid biosynthesis (Mano et al., 2007; Hichri et al., 2011).</p> <p> Among the MYB family TFs, MYB 4 and R2R3-MYB were highly abundant in <i>O. indicum</i> root (Table 6). R2R3-MYB protein is known to participate in the regulation of specialized metabolism including production of phenylpropanoids and flavonoids in plants (Vom Endt et al., 2002; Bomal et al., 2008; Taylor and Grotewold, 2005). The putative TF bHLH was highly expressed in the root transcriptome of <i>O. indicum.</i> bHLH interacts with R3 repeat domains of MYB proteins at the Nterminal acidic region to form the MYB –bHLH complex, involved in flavonoid biosynthesis pathway regulation (Feller et al., 2011). Transducin/WD-40 family isoform 5, of the WD40 family was abundant in <i>O. indicum</i> roots. WD40 proteins do not possess any catalytic activity, but it has been hypothesized that they act as a docking platform for regulating the anthocyanin and phenylalanine biosynthesis pathways (Feller et al., 2011).</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 205, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Advances in Physiological, Transcriptomic, Proteomic, Metabolomic, and Molecular Genetic Approaches for Enhancing Mango Fruit Quality
No full textMango (Mangifera indica L.) is a nutritionally
important fruit of high nutritive value, delicious in taste with an
attractive aroma. Due to their antioxidant and therapeutic potential,
mango fruits are receiving special attention in biochemical and pharmacognosy-based
studies. Fruit quality determines consumer’s acceptance, and
hence, understanding the physiological, biochemical, and molecular
basis of fruit development, maturity, ripening, and storage is essential.
Transcriptomic, metabolomic, proteomic, and molecular genetic approaches
have led to the identification of key genes, metabolites, protein
candidates, and quantitative trait loci that are associated with enhanced
mango fruit quality. The major pathways that determine the fruit quality
include amino acid metabolism, plant hormone signaling, carbohydrate
metabolism and transport, cell wall biosynthesis and degradation,
flavonoid and anthocyanin biosynthesis, and carotenoid metabolism.
Expression of the polygalacturonase, cutin synthase, pectin methyl
esterase, pectate lyase, β-galactosidase, and ethylene biosynthesis
enzymes are related to mango fruit ripening, flavor, firmness, softening,
and other quality processes, while genes involved in the MAPK signaling
pathway, heat shock proteins, hormone signaling, and phenylpropanoid
biosynthesis are associated with diseases. Metabolomics identified
volatiles, organic acids, amino acids, and various other compounds
that determine the characteristic flavor and aroma of the mango fruit.
Molecular markers differentiate the mango cultivars based on their
geographical origins. Genetic linkage maps and quantitative trait
loci studies identified regions in the genome that are associated
with economically important traits. The review summarizes the applications
of omics techniques and their potential applications toward understanding
mango fruit physiology and their usefulness in future mango breeding
Cold-induced sweetening in potato (Solanum tuberosum L.): genetic analysis of the apoplastic invertase inhibitor gene
No full textPotatoes are increasingly consumed in the form of processed foodstuffs such as French fries and crisps. After harvest, potatoes need to be kept at low temperature to prevent sprouting during storage for round-the-year processing. However, tubers accumulate reducing sugars at low temperatures, a phenomenon referred to as cold-induced sweetening (CIS). The processing of these high sugar potatoes into crisps or fries leads to a dark brown to black product that renders them unfit for human consumption and causes a great loss to the processing industry. To prevent sprouting and diseases, chemical treatments have been applied to tubers in storage. The recent withdrawal of these chemicals has increased the reliance on cold storage for potato tubers and highlighted the importance of CIS. Extensive research is required to produce a cultivar resistant to cold induced sweetening (CIS) along with good processing quality. The present work focused on increasing the understanding of the biological processes (physiological, biochemical and molecular) contributing to the initiation and/or controlling of CIS in potato tubers. The genetic basis of this trait was examined in progeny from a cross between potato cultivars with poor and excellent CIS response. This included molecular markers for candidate genes of known position on potato chromosomes to assess the role of different alleles involved in carbohydrate metabolism. Association studies between marker alleles and the phenotype of the progeny were performed. Among all the candidate genes, allele diversity for apoplastic invertase inhibitor gene was further studied from resistant and susceptible potato cultivars. In total five alleles were identified. Polymorphism was observed in both exon and intron regions. Three alleles had a unique substitution at the predicted junction of the signal peptide and mature protein. In order to identify the specific alleles that may play a role in resistance to CIS, transgenic potato plants have been produced with overexpression and antisense repression of apoplastic invertase inhibitor alleles. The results revealed that there were no consistent differences in CIS traits among the transgenic lines with the various alleles. However, the results of the transcript analysis showed much higher and stable transcripts levels of the apoplastic invertase inhibitor in the 1021/1 derived transgenic lines. This greater accumulation or stability of the apoplastic invertase inhibitor transcripts in 1021/1 may be a key factor contributing to the CIS trait of this cultivar.
A key difference from previous studies involves the use of 1021/1, a potato cultivar known to have the very high resistance to CIS. This study provided to help identify key genes for the future genetic improvement of tuber properties with respect to long-term storage and processing characteristics. The development of a potato that does not sweeten in the cold will revolutionize the potato industry as this problem currently contributes 20 percent losses after crop harvest. Once identified, clones resistance to CIS could be used in potato breeding programmes for the development of cold-resistant processing cultivars. Eliminating the need for chemical application of sprout inhibitors will be helpful to develop sustainable approaches to benefit both mankind and potato industries. These biotechnological tools will be used to identify elite potatoes with improved properties of the tuber with respect to long-term storage and processing characteristics (cold-sweetening and after-cooking darkening)
Oroxylum indicum subsp. root
No full text<i>2.7. Expression pattern of selected phenylpropanoid and flavonoid</i> <i>biosynthesis pathway genes in the young and mature roots of O. indicum</i> <p> Relative expression levels of seven genes namely, cinnamyl alcohol dehydrogenase (<i>OinCAD</i>), 4-coumarate–CoA ligase (<i>Oin4CL</i>), transcinnamate 4-monooxygenase (<i>OinC4H</i>), chalcone synthase (<i>OinCHS</i>), flavone synthase (<i>OinFNS</i>), chalcone isomerase (<i>OinCHI</i>) and flavanone 3-dioxygenase (<i>OinF3H</i>) were determined by a quantitative real time polymerase chain reaction (qRT-PCR) (Fig. 4) in young and old roots of <i>O. indicum</i>. The expression level of <i>OinCAD</i> was not significantly different in the two tissues. A two fold higher expression of <i>Oin4CL</i> was detected in old roots as compared to young roots. The expression of <i>OinC4H</i> was lower in both the young and old root of <i>O. indicum</i>. <i>OinCHS</i> showed around a four fold higher expression in the old root as compared to the young root (Fig. 4). <i>CHS</i> is the first rate-limiting enzyme in flavonoid biosynthesis pathway and higher levels of the enzyme is directly correlated with the higher level of flavonoids (Zuk et al., 2016). On the contrary, expression of <i>OinCHI</i>, <i>OinFNS</i> and <i>OinF3H</i> were at least ten fold higher in young roots as compared to old roots of <i>O. indicum</i> (Fig. 4). The higher expression of <i>CHI</i> in young roots may be linked to its role in auxin movement leading to plant growth and development (Peer and Murphy, 2007). Moreover, there are possibly different isoforms of the flavonoid biosynthesis genes which display spatial and temporal regulation, as reflected by their differential expression in young and old roots of <i>O. indicum</i>.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 206, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Oroxylum indicum subsp. root
No full text<p> <i>2.8. Identification and phylogenetic analysis of cytochrome P 450s</i> <i>(CYP450s) putatively involved in biosynthesis of specialized flavonoids like baicalein in O. indicum root</i></p> <p> Command line BLAST was performed on the <i>O. indicum</i> transcriptome using flavone synthase II, flavone-6-hydroxylase, glucuronidase and transferase genes reported from <i>Scutellaria baicalensis</i> and shown to be involved in the biosynthesis of specialized flavonoids. This led to the identification of the <i>O. indicum</i> homologs of those genes as listed (Table 7). Additionally, 164 transcripts annotated as <i>CYP 4</i> 50s from <i>O. indicum</i> transcriptome were analyzed (Supplementary Table 4.) Of these, the ones with high FPKM value (more than 5.5), were screened for identification of full length CYP450 ORFs from the <i>O. indicum</i> root transcriptome. A total of 31 genes (<i>OinCyp450</i>) were identified (Table 8). The phylogenetic tree of these <i>OinCyp 4</i> 50s indicated a high diversity of CYP450s in the <i>O. indicum</i> root (Fig. 5). At least five <i>OinCyps</i> showed a high degree of similarity to biochemically well characterized enzymes from <i>S. baicalensis</i> namely, flavones synthase II, baicalin-ss-D-glucuronidase, flavone-6-hydroxylase, baicalin-7-O-glucuronosyltransferase (Liu et al., 2015; Zhao et al., 2016, 2018). These enzymes catalyze the biosynthesis of specialized flavonoids like baicalin and wogonin through a root specific alternative pathway (Zhao et al., 2016).</p> <p> The <i>OinCyp3</i> and <i>OinCyp4</i> were abundant in roots of <i>O. indicum</i> and showed a high degree of similarity with flavone synthase II (CYP93B; Zhao et al., 2016) along with five more <i>OinCyps</i> (Fig. 5). Moreover, OinCyp2 (with similarity to <i>S. baicalensis</i> baicalin-ss-D-glucuronidase) clustered close to OinCyp27. OinCyp2 and OinCyp35 (both flavone-6- hydroxylase) clustered away from each other forming two different OinCyp clades (Fig. 5). OinCyp5 (with similarity to <i>S. baicalensis</i> baicalin-7-O-glucuronosyl transferase) was highly abundant in <i>O. indicum</i> roots and formed a cluster with at least five more OinCyps. Based on the phylogenetic analysis of the OinCyps, it can be hypothesized that they are involved in the specialized flavonoid biosynthesis in <i>O. indicum</i> roots. Further, the functional validation of OinCyps may highlight their specific biochemical roles in metabolite biosynthesis in <i>O. indicum</i>.</p> <p> Phylogenetic variations in <i>Cyp450</i> genes play a central role in evolution of metabolic complexity (Bak et al., 2011). <i>Cyp9</i> 8 A and its duplicated sister genes evolved functional diversification in phenolic and flavonoid biosynthesis pathways (Liu et al., 2016). The flavonoid biosynthesis pathway is known to involve the formation of metabolons or protein complexes (Bassard et al., 2017). It has been demonstrated that Cyp450s like flavone synthase and cinnamate 4-hydroxylase are ER membrane anchored enzymes and provide a nucleation platform for the assembly of other soluble enzymes like chalcone synthase, chalcone isomerase and reductase. Together, these complexes drive the flavonoid metabolism (Dastmalchi et al., 2016) and plant specific diversity in a flavonoid metabolon organization (Fujino et al., 2018). Detailed functional validation of OinCyp diversity will open up their precise biochemical roles and novelty in specialized flavonoid metabolism in <i>O. indicum</i>.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 206, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
