Understanding plant stress memory traits can provide a way for sustainable agriculture.

Being sessile, plants encounter various biotic and abiotic threats in their life cycle. To minimize the damages caused by such threats, plants have acquired sophisticated response mechanisms. One major such response includes memorizing the encountered stimuli in the form of a metabolite, hormone, protein, or epigenetic marks. All of these individually as well as together, facilitate effective transcriptional and post-transcriptional responses upon encountering the stress episode for a second time during the life cycle and in some instances even in the future generations. This review attempts to highlight the recent advances in the area of plant memory. A detailed understanding of plant memory has the potential to offer solutions for developing climate-resilient crops for sustainable agriculture.

CircRNAs responsive to winter dormancy and spring flushing conditions of tea leaf buds.

Circular RNAs (circRNAs) are important regulators of diverse biological processes of plants. However, the evolution and potential functions of circRNAs during winter dormancy and spring bud flushing of tea plant is largely unknown. Using RNA-seq data, a total of 1184 circRNAs were identified in the winter dormant and spring bud flushing leaf samples of tea plants in two different cultivars exhibiting different duration of winter dormancy. A total of 156 circRNAs are found to be differentially expressed and the weighted gene co-expression network (WGCNA) analysis revealed that 22 and 20 differentially expressed-circRNAs (DE-circRNAs) positively correlated with the flushing and dormant leaf traits, respectively, in both the tea cultivars used. Some transcription factors (TFs) viz. MYB, WRKY, ERF, bHLH and several genes related to secondary metabolite biosynthetic pathways are found to co-express with circRNAs. DE-circRNAs also predicted to interact with miRNAs and can regulate phytohormone biosynthesis and various signalling pathways in tea plant. This study uncovers the potential roles of circRNAs to determine winter dormancy and spring bud flushing conditions in tea plants.

Plant and soil-associated microbiome dynamics determine the fate of bacterial wilt pathogen Ralstonia solanacearum.

MAIN CONCLUSION: Plant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants. Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant-microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community.

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

Evaluation of seed associated endophytic bacteria from tolerant chilli cv. Firingi Jolokia for their biocontrol potential against bacterial wilt disease.

In this study, the seed endosphere of a bacterial wilt tolerant chilli cv. Firingi Jolokia was explored in order to find effective agents for bacterial wilt disease biocontrol. A total of 32 endophytic bacteria were isolated from freshly collected seeds and six isolates were selected based on R. solanacearum inhibition assay. These isolates were identified as Bacillus subtilis (KJ-2), Bacillus velezensis (KJ-4), Leuconostoc mesenteroides (KP-1), Lactococcus lactis (LB-3), Bacillus amyloliquefaciens (WK-2), and Bacillus subtilis (WK-3) by 16S rRNA gene sequencing. In the in planta R. solanacearum inhibition assay carried out by seedling root bacterization method, Bacillus subtilis (KJ-2) exhibited highest biocontrol efficacy of 86.6 % on 7th day post R. solanacearum inoculation and a minimum biocontrol efficacy of 52.9 % was noted for Leuconostoc mesenteroides (KP-1). GC-HRMS analysis detected several known antimicrobial compounds in the extract of the culture supernatant of Bacillus subtilis (KJ-2); which may contribute to inhibition of R. solanacearum. In the growth promotion assay conducted using these isolates, only two of them namely Bacillus subtilis (KJ-2) and Bacillus amyloliquefaciens (WK-2) showed growth promotion in true leafed tomato plants. All the selected seed endophytic isolates were able to control bacterial wilt of tomato at the seedling stage and Bacillus subtilis (KJ-2) was found to be most effective in controlling the disease. The results of the present study highlighted that seed endosphere of bacterial wilt tolerant cultivar is a rich source of R. solanacearum antagonizing bacterial isolates.

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea.

Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.

Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions.

Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant's defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum.

Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.

Understanding the role of miRNAs for improvement of tea quality and stress tolerance.

MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs that exhibit important role in regulation of gene expression, mostly through the mechanism of cleavage and/or inhibition of translation of target mRNAs during or after transcription. Although much has been unravelled about the role of miRNAs in diverse biological processes like maintenance of functional integrity of genes and genome, growth and development, metabolism, and adaptive responses towards biotic and abiotic stresses in plants, not much is known on their specific roles in majority of cash crops - an area of investigation with potentially significant and gainful economic implications. Tea (Camellia sinensis) is globally the second most consumed beverage after water and its cultivation has major agro-economic and social ramifications. In recent years, global tea production has been greatly challenged by many biotic and abiotic stress factors and a deeper understanding of molecular processes regulating stress adaptation in this largely under investigated crop stands to significantly facilitate potential crop improvement strategies towards durable stress tolerance. This review endeavours to highlight recent advances in our understanding of the role of miRNAs in regulating stress tolerance traits in tea plant with additional focus on their role in determining tea quality attributes.

Identification of putative miRNAs from expressed sequence tags of Gnetum gnemon L. and their cross-kingdom targets.

Wild edible plants are often found to be rich sources of nutrients and medicinally beneficial compounds with pharmacological activities. Gnetum gnemon is a nutritionally important plant and a popular food source in parts of Assam and North-East India. Various microRNAs (miRNAs) have been recently identified in many plants; however, there are no records of identification of miRNAs in any species of Gnetum. The prediction of miRNA-target associations in G. gnemon is an important step to facilitate functional genomics studies in this species. In the present study, all known miRNAs from plants available in public domain were used to search for the conserved G. gnemon miRNA homologues in publicly accessible expressed sequence tags (ESTs) in NCBI database. An aggregate of 20 new potential miRNAs belonging to two diverse miRNA families (miR399 and miR5021) were identified through a homology-based search by following stringent filtering criteria. To investigate the potential cross-kingdom effects of the identified miRNAs, we further identified the putative target genes of G. gnemon miRNAs in human transcriptome and analyzed them against the NCBI non-redundant protein database. The KEGG analysis of the target genes indicated that these genes were involved in different metabolic pathways such as caffeine metabolism, drug metabolism, and nitrotoluene degradation. The target genes of G. gnemon miRNAs in humans were found to be associated with various disorders of both hereditary and non-hereditary origin. These results could help to shed new light on understanding of miRNA-mRNAs functional networks in this species and its potential use as a small RNA-based therapy against some human diseases.

Endophytes from Gnetum gnemon L. can protect seedlings against the infection of phytopathogenic bacterium Ralstonia solanacearum as well as promote plant growth in tomato.

Endophytes are beneficial plant microbes which help the plants by producing various plant growth promoting substances and also by acting as biocontrol agents against various plant pathogens. In the present study, evaluation of endophytic bacteria isolated from Gnetum gnemon, an ethnomedicinal plant was carried out for their plant growth promoting (PGP) activity and antagonistic potential against bacterial wilt pathogen Ralstonia solanacearum. Initially a total of 40 endophytic bacteria were isolated which were clustered into 13 groups based on RFLP and BOX-PCR fingerprinting. These 13 representative isolates belonged to different genera of Bacillus (9), Solibacillus (1), Staphylococcus (2) and Caballeronia (1). Among them, six isolates were positive for production of IAA, the value of which ranged from 11.16 to 27.63 µg mL-1. Phosphate solubilisation in the range of 106.4 to -212.7 µg mL-1 was shown by three isolates. Eight isolates producedammonia, the value of which ranged from 1.3 to 6.1 µmol mL-1. All tested isolates were positive for siderophore production. For extracellular enzyme production, 7 isolates were positive for protease, 8 for cellulase and 10 for amylase production. The isolates were also tested for their antagonistic activity against R. solanacearum in vitro and in planta assay using tomato seedlings. Staphylococcus warneri GL1 showed the highest biocontrol efficacy of 77.67 % followed by Bacillus velezensis GL3 i.e. 70.1 %. R. solanacearum antagonistic isolates were analysed for the presence of antimicrobial peptide biosynthesis genes bmyB, srfAA, fenD and ituC. All the antagonistic isolates showed the presence of all four genes, except the isolate Bacillus velezensis GMC2, where the gene for fengycin synthetase (fenD) was absent. Based on in vitro PGP traits, three isolates Bacillus velezensis GL3, Bacillus atrophaeus GMC1 and Bacillus megaterium GS2 were selected, these three endophytic bacteria individually and their consortia were tested for in planta PGP activities in tomato plants. Application of Bacillus velezensis GL3 alone and consortia of three isolates showed significant improvement in growth parameters such as shoot length, fresh weight and dry weight in a pot experiment. Colonization of endosphere of treated tomato seedlings by the endophytic isolate Bacillus velezensis GL3 was confirmed by visualization of colony morphology and BOX-PCR fingerprinting. Our study highlights the potential of endophytes associated with unexplored plants like G. gnemon for development of bioformulation aimed at enhancing plant growth and bacterial wilt disease control.

Mining of miRNAs from EST data in Dendrobium nobile.

Dendrobium nobile is an orchid species highly popular for its therapeutic properties and is often used as a medicinal herb. Documenting miRNA-target associations in D. nobile is an important step to facilitate functional genomics studies in this species. Therefore, it is of interest to identify miRNA sequences from EST data available in public databases using known techniques and tools. We report 14 potential miRNAs from three ESTs of D. nobile. They belong to 3 miRNA families (miR390, miR528 and miR414) linking to transcription factor regulation, signal transduction, DNA and protein binding, and various cellular processes covering 34 different metabolic networks in KEGG. These results help in the understanding of miRNA-mRNAs functional networks in Dendrobium nobile.

Coinfections as an aetiology of acute undifferentiated febrile illness among adult patients in the sub-Himalayan region of north India.

BACKGROUND & OBJECTIVES: In India, certain geographic regions witness simultaneous outbreaks of two or more diseases like scrub typhus, dengue fever, malaria, leptospirosis and chikungunya during monsoon and post-monsoon period, sharing common indication of acute febrile illness. The objective of the present study was to assess the prevalence of coinfections among patients with acute undifferentiated fevers (AUF) admitted in a tertiary care hospital in the northern hilly state of Himachal Pradesh, India. METHODS: This was a hospital based open cohort study conducted over a period of two months (September and October) in 2016. All the patients above the age of 18 yr admitted in medical wards and fulfilling the definition of AUF were included. The patients diagnosed with dual infections were the subjects of the study. Standard guidelines were used for case definitions of scrub typhus, dengue, chikungunya, malaria and leptospirosis. RESULTS: Dual infections were noted in 16 patients admitted with AUF. The most common coinfection was scrub typhus and dengue, reported in 10 patients. Scrub typhus and leptospirosis coinfection was observed in three patients. Dengue and chikungunya was observed in one patient. Scrub typhus, dengue and vivax malaria was detected in one patient. Scrub typhus and vivax malaria was detected in one patient. Out of the 10 cases positive for both scrub and dengue, four had no history of travel outside Himachal Pradesh. All three cases positive for both scrub and leptospirosis were indigenous without any history of travel outside Kangra, Himachal Pradesh. The outcome of all the patients was with full recovery. INTERPRETATION & CONCLUSION: The study established the presence of coinfections (mainly dengue fever and leptospirosis) as a cause of AUF in the study area, which is a nonendemic region. The role of easily available and widely performed serological tests in the aetiological diagnosis of AUF is significant. Studies are required to determine the normal titres in the local population before using the imported commercially available serological tests in the diagnosis of AUF.

Draft Genome Sequence of a Polymyxin B-Resistant Sequence Type 195 Clinical Isolate of Acinetobacter baumannii from India.

Acinetobacter baumannii has emerged as a troublesome nosocomial pathogen worldwide. We report here the draft genome sequence of polymyxin B-resistant sequence type 195 (ST195) A. baumannii strain GU71, isolated from a tertiary care hospital in the city of Guwahati, Assam, India.