@article { ISI:000365070700106, title = {Two new potential barcodes to discriminate dalbergia species}, journal = {Plos One}, volume = {10}, number = {11}, year = {2015}, month = {NOV}, pages = {Article Number: e0142965}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {

DNA barcoding enables precise identification of species from analysis of unique DNA sequence of a target gene. The present study was undertaken to develop barcodes for different species of the genus Dalbergia, an economically important timber plant and is widely distributed in the tropics. Ten Dalbergia species selected from the Western Ghats of India were evaluated using three regions in the plastid genome (matK, rbcL, trnH-psbA), a nuclear transcribed spacer (nrITS) and their combinations, in order to discriminate them at species level. Five criteria: (i) inter and intraspecific distances, (ii) Neighbor Joining (NJ) trees, (iii) Best Match (BM) and Best Close Match (BCM), (iv) character based rank test and (v) Wilcoxon signed rank test were used for species discrimination. Among the evaluated loci, rbcL had the highest success rate for amplification and sequencing (97.6\%), followed by matK (97.0\%), trnH-psbA (94.7\%) and nrITS (80.5\%). The inter and intraspecific distances, along with Wilcoxon signed rank test, indicated a higher divergence for nrITS. The BM and BCM approaches revealed the highest rate of correct species identification (100\%) with matK, matK+rbcL and matK+trnH-psb loci. These three loci, along with nrITS, were further supported by character based identification method. Considering the overall performance of these loci and their ranking with different approaches, we suggest matK and matK+rbcL as the most suitable barcodes to unambiguously differentiate Dalbergia species. These findings will potentially be helpful in delineating the various species of Dalbergia genus, as well as other related genera.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0142965}, author = {Bhagwat, Rasika M. and Dholakia, Bhushan B. and Kadoo, Narendra Y. and Balasundaran, M. and Gupta, Vidya S.} } @article {43799, title = {Transcriptional transitions in alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {AUG}, type = {Article}, abstract = {Alphonso is known as the "King of mangos" due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation ( p-value <= 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.}, doi = {10.1038/s41598-017-08499-5}, author = {Deshpande, Ashish B. and Anamika, Krishanpal and Jha, Vineet and Chidley, Hemangi G. and Oak, Pranjali S. and Kadoo, Narendra Y. and Pujari, Keshav H. and Giri, Ashok P. and Gupta, Vidya S.} } @article {46123, title = {Transcriptomics analysis of propiconazole-treated Cochliobolus sativus reveals new putative azole targets in the plant pathogen}, journal = {Functional \& Integrative Genomics}, volume = {19}, year = {2019}, month = {MAY}, pages = {453-465}, type = {Article}, abstract = {

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is a filamentous fungus from the class Dothideomycetes. It is a pathogen of cereals including wheat and barley, and causes foliar spot blotch, root rot, black point on grains, head blight, leaf blight, and seedling blight diseases. Annual yields of these economically important cereals are severely reduced due to this pathogen attack. Evolution of fungicide resistant pathogen strains, availability of a limited number of potent antifungal compounds, and their efficacy are the acute issues in field management of phytopathogenic fungi. Propiconazole is a widely used azole fungicide to control the disease in fields. The known targets of azoles are the demethylase enzymes involved in ergosterol biosynthesis. Nonetheless, azoles have multiple modes of action, some of which have not been explored yet. Identifying the off-target effects of fungicides by dissecting gene expression profiles in response to them can provide insights into their modes of action and possible mechanisms of fungicide resistance. Moreover it can also reveal additional targets for development of new fungicides. Hence, we analyzed the global gene expression profile of C. sativus on exposure to sub-lethal doses of propiconazole in a time series. The gene expression patterns were confirmed using quantitative reverse transcriptase PCR (qRT-PCR). This study revealed overexpression of target genes from the sterol biosynthesis pathway supporting the reported mode of resistance against azoles. In addition, some new potential targets have also been identified, which could be explored to develop new fungicides and plant protection strategies.

}, keywords = {Bipolaris sorokiniana, Cochliobolus sativus, Fungicide resistance, Propiconazole, RNA-seq, Transcriptomics analysis}, issn = {1438-793X}, doi = {10.1007/s10142-019-00660-9}, author = {Somani, Deepika and Adhav, Ragini and Prashant, Ramya and Kadoo, Narendra Y.} } @article {49702, title = {Transcriptome analyses reveal TaWRKY41 as a potential candidate governing spot blotch resistance in wheat}, journal = {Physiology and Molecular Biology of Plants}, volume = {31}, year = {2025}, month = {APR}, pages = {591-608}, type = {Article}, abstract = {

Spot blotch disease caused by Bipolaris sorokiniana poses a significant threat to wheat production. Cultivation of disease-resistant wheat genotypes appears to be the most practical approach to mitigate the impact of this devastating disease. However, the molecular responses of wheat plants during spot blotch disease progression remain poorly understood. This study employed RNA-sequencing to unravel the spatiotemporal molecular events underlying the resistance mechanism in the spot blotch susceptible and resistant wheat genotypes. This study further provides a comprehensive overview of differentially expressed transcripts through functional analysis and transcription factor identification, elucidating the biological mechanisms governing wheat-B. sorokiniana interaction. In the resistant genotype, the expression of one of the key transcription factors, TaWRKY41, was significantly induced upon pathogen inoculation. Computational studies, electrophoretic-mobility shift assay, and yeast one-hybrid assay confirmed the interaction of the recombinant TaWRKY41 protein with W-box elements present in the promoters of plant defense-related genes. Furthermore, co-expression network analyses identified downstream genes positively correlated with TaWRKY41, providing insights into their probable involvement in the defense response. Overall, our investigation suggests that TaWRKY41 contributes to spot blotch resistance in wheat. This knowledge can help develop new disease-resistant wheat varieties.

}, keywords = {Plant defense, plant-pathogen interaction, TaWRKY41, Transcription factors, Transcriptomics}, issn = {0971-5894}, doi = {10.1007/s12298-025-01583-5}, author = {Dayama, Bhakti R. and Mahadik, Varsha A. and Somani, Deepika and Shinde, Balkrishna A. and Kondhare, Kirtikumar R. and Karthikeyan, Muthukumarasamy and Kadoo, Narendra Y.} }