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Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR ( http://backlin.cabgrid.res.in/tiger/ ), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.
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Basidiomycota , Enfermedades de las Plantas , Transcriptoma , Triticum , Triticum/genética , Triticum/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Basidiomycota/patogenicidad , Basidiomycota/fisiología , Perfilación de la Expresión Génica , Genoma Fúngico , Interacciones Huésped-Patógeno/genéticaRESUMEN
BACKGROUND: Drought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% of Brassica juncea (Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87 B. carinata-derived B. juncea introgression lines (ILs) was developed with the goal of creating drought-tolerant genotypes. METHOD: The experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map. RESULTS: The linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed by B. carinata (BC 4), suggesting a greater contribution of B. carinata towards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome of B. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz., SOS2, SOS2 like, NPR1, FAE1-KCS, HOT5, DNAJA1, NIA1, BRI1, RF21, ycf2, WRKY33, PAL, SAMS2, orf147, MAPK3, WRR1 and SUS, were reported in the genomic regions of identified QTLs. CONCLUSIONS: The significance of B. carinata in improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
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Resistencia a la Sequía , Sitios de Carácter Cuantitativo , Sitios de Carácter Cuantitativo/genética , Mapeo Cromosómico , Fenotipo , Genotipo , Planta de la Mostaza/genéticaRESUMEN
The relationship between diabetes mellitus (DM) and high serum uric acid is complex and controversial. Many epidemiological studies have reported a positive association, whereas others have reported an inverse association or none. In the pathogenesis of DM it is the intracellular urate that is more important than the extracellular and dissociation between the two is possible. Evidence suggests that high serum uric acid induces insulin resistance and beta cell failure in animal models. Reduction of intracellular uric acid can be achieved by dietary measures such as reducing fructose and salt intake, and uric acid-lowering drugs. We suggest that in the Western diet, these elements play a crucial role in pathogenesis of DM. To determine the precise and exact interrelationship between intracellular and extracellular uric acid, well-designed studies are required. Besides this, clinical trials are needed to determine whether intracellular and extracellular urate reduction will provide benefit in prevention and treatment of DM and complications associated with it.
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Diabetes Mellitus , Resistencia a la Insulina , Animales , Humanos , Ácido Úrico , Diabetes Mellitus/tratamiento farmacológicoRESUMEN
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Cucumis sativus , Biología , Clorofila/metabolismo , Cucumis sativus/genética , Frutas/genética , Frutas/metabolismo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , GenotipoRESUMEN
Spotted stem borer, Chilo partellus, is the most important constraint for increasing the production and productivity of maize and sorghum, the two major coarse cereals in Asia and Africa. The levels of resistance to this pest in the cultivated germplasm are low to moderate, and hence, farmers have to use insecticides for effective control of this pest. However, there is no information on the detoxification mechanisms in C. partellus, which is one of the constraints for deployment of appropriate insecticides to control this pest. The ability to detoxify insecticides varies across insect populations, and hence, we sequenced different populations of C. partellus to identify and understand detoxification mechanisms to devise appropriate strategies for deployment of different insecticides for controlling this pest. Larval samples were sequenced from three different cohorts of C. partellus using the Illumina HiSeq 2500 platform. The data were subjected to identify putative genes that are involved in detoxification on insecticides in our cohort insect species. These studies resulted in identification of 64 cytochrome P450 genes (CYP450s), and 36 glutathione S-transferases genes (GSTs) encoding metabolic detoxification enzymes, primarily responsible for xenobiotic metabolism in insects. A total of 183 circadian genes with > 80% homolog and 11 olfactory receptor genes that mediate chemical cues were found in the C. partellus genome. Also, target receptors related to insecticide action, 4 acetylcholinesterase (AChE), 14 γ-aminobutyric acid (GABA), and 15 nicotinic acetylcholine (nAChR) receptors were detected. This is the first report of whole genome sequencing of C. partellus useful for understanding mode of action of different insecticides, and mechanisms of detoxification and designing target-specific insecticides to develop appropriate strategies to control C. partellus for sustainable crop production.
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Genoma de los Insectos , Insecticidas , Mariposas Nocturnas , Acetilcolinesterasa/genética , Animales , Grano Comestible , Insecticidas/toxicidad , Mariposas Nocturnas/efectos de los fármacos , Mariposas Nocturnas/genética , Secuenciación Completa del Genoma , Zea maysRESUMEN
Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.
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Microbiota , Animales , Antibacterianos , Bacterias , ADN Ribosómico , ARN Ribosómico 16S/genéticaRESUMEN
BACKGROUND: Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT: A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION: This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Carpas , Cyprinidae , Animales , Cyprinidae/genética , Femenino , Placenta , Embarazo , Reproducción/genética , Análisis de Secuencia de ARNRESUMEN
Black pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought-affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine-rich repeats and ubiquitin-like domain), serine threonine protein kinase, Mitogen-activated protein kinase, Nucleotide Binding Site-Leucine Rich Repeat, Myeloblastosis-related proteins, basic helix-loop-helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http://webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop drought-tolerant variety for better black pepper productivity.
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Piper nigrum , Sequías , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Piper nigrum/genética , Transcriptoma/genéticaRESUMEN
Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.
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Elettaria/genética , Genoma de Planta , Interacciones Huésped-Patógeno , Transcriptoma , Elettaria/virología , Regulación de la Expresión Génica de las Plantas , Mutación INDEL , Repeticiones de Microsatélite , Virus del Mosaico/patogenicidad , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/virología , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Polimorfismo de Nucleótido Simple , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
A massive bovine, Bos frontalis, also known as Mithun or Gayal, found at higher altitude is very promising meat and milk animal. For candidate gene and marker discovery, RNA-seq data was generated from longissimus dorsi muscle tissues with Illumina-HiSeq. Such markers can be used in future for genetic gain of traits like feed conversion efficiency (FCE) and average daily gain (ADG). Analysis revealed 297differentially expressed genes (DEGs) having 173 up and 124 down-regulated unigenes. Extensive conservation was found in genic region while comparing with Bos taurus. Analysis revealed 57 pathways having 112 enzymes, 72 transcriptional factors and cofactors, 212 miRNAs regulating 71 DEGs, 25,855 SSRs, mithun-specific 104,822 variants and 7288 indels, gene regulatory network (GRN) having 24 hub-genes and transcriptional factors regulating cell proliferation, immune tolerance and myogenesis. This is first report of muscle transcriptome depicting candidate genes with GRN controlling FCE and ADG. Reported putative molecular markers, candidate genes and hub proteins can be valuable genomic resources for association studies in genetic improvement programme.
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Bovinos/genética , Redes Reguladoras de Genes , Músculos/metabolismo , Transcriptoma , Animales , Ontología de Genes , Mutación INDEL , MicroARNs/metabolismo , Repeticiones de Microsatélite , Polimorfismo de Nucleótido SimpleRESUMEN
The role of microRNA in gene regulation during developmental biology has been well depicted in several organisms. The present study was performed to investigate miRNAs role in the liver tissues during carbohydrate metabolism and their targets in the farmed carp rohu, Labeo rohita, which is economically important species in aquaculture. Using Illumina-HiSeq technology, a total of 22,612,316; 44,316,046 and 13,338,434 clean reads were obtained from three small-RNA libraries. We have identified 138 conserved and 161 novel miRNAs and studies revealed that miR-22, miR-122, miR-365, miR-200, and miR-146 are involved in carbohydrate metabolism. Further analysis depicted mature miRNA and their predicted target sites in genes that were involved in developmental biology, cellular activities, transportation, etc. This is the first report of the presence of miRNAs in liver tissue of rohu and their comparative profile linked with metabolism serves as a vital resource as a biomarker.
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Metabolismo de los Hidratos de Carbono/genética , Carpas/genética , Hígado/metabolismo , MicroARNs/metabolismo , Animales , Carpas/metabolismo , Carbohidratos de la Dieta/administración & dosificación , Regulación de la Expresión Génica , Ontología de Genes , ARN Mensajero/metabolismo , RNA-SeqRESUMEN
Though the volatile profiles of black pepper have been reported already, the information on terpene synthase family genes is not known. In this study, using a combinatorial approach, the berry hybrid transcriptome assembly of llumina and nanopore sequencing, the entire terpene synthase family responsible for the biosynthesis of the flavor-imparting volatiles in black pepper berries was profiled. The profile shows 98 terpene synthases from various terpene synthesis pathways. Three important monoterpene synthases were also validated by targeted amplification, sequencing and homology modeling. This study provides the first of its kind information on the terpene synthase family profile in Piper nigrum, which is potentially a major step for further characterization of the functional terpene synthase genes in black pepper. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00986-4.
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Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder's Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~ 50%), A (~ 39%), and D (~ 10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon's information index (I) = 0.648, expected heterozygosity (He) = 0.456 and unbiased expected heterozygosity (uHe) = 0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.
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Triticum/genética , Triticum/metabolismo , Mapeo Cromosómico/métodos , Cromosomas de las Plantas/genética , Grano Comestible/genética , Variación Genética/genética , Genoma de Planta/genética , Estudio de Asociación del Genoma Completo/métodos , Genotipo , Fenotipo , Fitomejoramiento/métodos , Poaceae/genética , Polimorfismo de Nucleótido Simple/genéticaRESUMEN
Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved 'Jayanti rohu' Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPARγ. The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose efficiency in carp species, for sustainable and cost-effective aquaculture production.
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Animales Modificados Genéticamente/metabolismo , Carpas/metabolismo , Dieta de Carga de Carbohidratos/efectos adversos , Hígado/metabolismo , Análisis de Secuencia de ARN/métodos , Animales , Animales Modificados Genéticamente/genética , Acuicultura/métodos , Metabolismo de los Hidratos de Carbono , Carpas/genética , Regulación de la Expresión Génica , Hígado/patología , Transducción de Señal , TranscriptomaRESUMEN
The present study was aimed to analyse bioactive compounds (total phenolics, ascorbic acid and sinigrin) and antioxidant activity in 14 mid-early cauliflower genotypes. Significant differences (pb 0.05) were observed among the genotypes for all bioactive compounds and antioxidant activity. Total phenolics content of curd were ranged from 20.36 to 48.93 mg gallic acid equivalent (GAE) 100 g-1 fresh weight (FW) which showed 2.5 times variation. The ascorbic acid content was maximum in DC522 (88.53 mg 100 g-1 FW) followed by Pusa Sharad (65.64 mg 100 g-1 FW) while minimum in DC310 (39.62 65.64 mg 100 g-1 FW). Wide variation was observed for cupric reducing antioxidant capacity and ferric reducing antioxidant power ranging from 9.04 to 20.83 mg GAE 100 g-1 FW and 13.11 to 26.31 mg GAE 100 g-1 FW, respectively. Sinigrin was found to be highest in DC306 (39.50 µmol 100 g-1 FW) for leaf and in DC326 (36.93 µmol 100 g-1 FW) for curd sample. The cauliflower genotypes were classified based on chemometric approaches namely principal component analysis (PCA) and agglomerative hierarchical clustering (AHC). The first two principal components (PC1 and PC2) explained 50.62% and 23.28% of total variance, respectively. The AHC as revealed by heat map classified cauliflower genotypes into four main groups based on measured traits. The information is useful for developing varieties and/or hybrids rich in bioactive compounds and antioxidant activity.
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Blueberry fruits are known for their high vitamin C, essential dietary fibre, antioxidant activity and anthocyanin pigments. Different blueberry varieties have been introduced in India but no attempt has been made for their nutritional profiling. Nutritional profiling of varieties helps us to know the unique varietal characters, which serves as a guideline for recommendation of a valuable variety for fresh consumption and/or processing. Therefore, the present study was conducted in eight different blueberry varieties such as 'Misty', 'Sharp Blue', 'Biloxi', 'Jewel', 'Gulf Coast', 'Blue Crop', 'Star', 'Legacy'. The results of the study revealed that all tested varieties differed significantly in physical attributes (10-berry weight, fruit firmness, roundness index, moisture content) and biochemical and functional attributes (ascorbic acid, total anthocyanin, total phenolic content, antioxidant activity, total sugars, organic acids) and mineral content. Regression analysis and Principal Component Analysis showed that antioxidant potential of blueberries was mainly contributed by phenolics followed by anthocyanins and ascorbic acid content. However for taste perception, fructose among sugars and succinic acid among sugars were the most influencing factors (p ≤ 0.05). Total phenolics and anthocyanins content were responsible for overall difference in functional attributes among the varieties. The attributes such as high fruit firmness, sensorial score, and appropriate shape and weight make 'Misty', the best variety for marketability and fresh consumption among all tested varieties.
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BACKGROUND: Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways. RESULTS: We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD. CONCLUSIONS: This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.
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Glycine max/genética , Enfermedades de las Plantas/genética , Proteínas de Plantas/genética , Transcriptoma/genéticaRESUMEN
The rise of New Delhi metallo-beta-lactamase-1 (NDM-1) producers is a major public health concern due to carbapenem resistance. Infections caused by carbapenem-resistant enterobacteria (CRE) are classified as a serious problem. To understand the structure and function of NDM-1, an amino acid replacement approach is considered as one of the methods to get structural insight. Therefore, we have generated novel mutations (N193A, S217A, G219A and T262A) near active sites and an omega-like loop to study the role of conserved residues of NDM-1. The minimum inhibitory concentrations (MICs) of ampicillin, imipenem, meropenem, cefotaxime, cefoxitin and ceftazidime for all mutants were found to be reduced 2 to 6 fold, compared to a wild type NDM-1 producing strain. The Km values increased while Kcat and Kcat/Km values were decreased compared to wild type. The affinity as well as the catalysis properties of these mutants were reduced considerably for imipenem, meropenem, cefotaxime, cefoxitin, and ceftazidimem compared to wild type, hence the catalytic efficiencies (Kcat/Km) of all mutant enzymes were reduced owing to the poor affinity of the enzyme. The IC50 values of these mutants with respect to each drug were reduced compared to wild type NDM-1. MD simulations and docking results from the mutant protein models, along with the wild type example, showed stable and consistent RMSD, RMSF and Rg behavior. The α-helix content values of all mutant proteins were reduced by 13%, 6%, 14% and 9% compared to NDM-1. Hence, this study revealed the impact role of active sites near residues on the enzyme catalytic activity of NDM-1.
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Antibacterianos/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , beta-Lactamasas/química , Antibacterianos/farmacología , Biocatálisis , Dominio Catalítico , Farmacorresistencia Bacteriana , Cinética , Pruebas de Sensibilidad Microbiana , Mutagénesis Sitio-Dirigida , Mutación , Unión Proteica , Estructura Secundaria de Proteína , Termodinámica , beta-Lactamasas/genética , beta-Lactamasas/metabolismoRESUMEN
Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement. Whole genome sequence of this crop is yet to be completed. Moreover, genomic resources are also not freely accessible, thus available transcriptome data can be of immense use. V. mungo Transcriptome database, accessible at http://webtom.cabgrid.res.in/vmtdb/ has been developed using available data of two contrasting varieties viz., cv. VM84 (resistant) and cv. T9 (susceptible). De novo assembly was carried out using Trinity and CAP3. Out of total 240,945 unigenes, 165,894 (68.8%) showed similarity with known genes against NR database, and remaining 31.2% were found to be novel. We found 22,101 differentially expressed genes in all datasets, 44,335 putative genic SSR markers, 4105 SNPs and Indels, 64,964 transcriptional factor, 546 mature miRNA target prediction in 703 differentially expressed unigenes and 137 pathways. MAPK, salicylic acid-binding protein 2-like, pathogenesis-related protein and NBS-LRR domain were found which may play an important role in defence against pathogens. This is the first web genomic resource of V. mungo for future genome annotation as well as ready to use markers for future variety improvement program.