The integrated metabarcoding and culturomic analysis of rice phyllosphere microbiome revealed the key role of environmental factor on shaping the structure and composition of phyllomicrobiome as compared to host genotype.

The core-microbiome analysis showed multi-microbiota-core consisting of genera namely Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces.

Rice phyllosphere associated bacterial isolates have shown antagonistic activity against blast fungus via secretory compound and volatile compound mediated antagonism activity. The phyllospheric bacteria induced defence elicitation in rice plant is identified as one of the possible mechanism for in blast disease suppression.

Potential bacterial candidate for microbiome re-engineering based plant disease management has been deciphered.

RNA seq analysis of root and floret tissue of bakanae disease susceptible rice genotype PB112 showed the altered expression of over 1000 genes involved in metabolism, signalling, environmental information processing and diverse biological activity.

Over 20 differentially expressed genes (DEGs) were found involved in development, morphogenesis, signalling and cellular metabolism.

Biocontrol mechanism of C. globosum against B. sorokiniana was deciphered by transcriptome sequences of 20-22 million reads (40.07Gb). The de novo assembly generated 45,582 transcripts with 27,957 unigenes representing 6109 differentially expressed genes. The transcripts classified as genes involved in “catalytic activity” constituted 45.06%, of which, 10.02 % were associated with hydrolytic activity and similarly in the biological process, 29.18% of transcripts were involved in metabolic activity. The results suggested an increase in the expression of genes encoding for secondary metabolites like polyketide synthase S-hydroxymethyl glutathione dehydrogenase, terpene cyclase, aminotran_1_2 domain-containing protein and other hydrolytic CAZYmes such as glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31 and GH 81, cellulase domain-containing protein, chitinases, β-1, 3-glucanases, glucan endo-1,3-beta-glucanase, and proteases.

The RNA-seq data was validated by RT-qPCR using 20 genes that confirmed the RNA-seq results.

The molecular cloning of AV2, AC2 and AC4 genes of ToLCNDV were cloned and functionally characterized. Proteins product of these genes act as a suppressor of RNA silencing as evidenced by a GUS reporter-silencing assay system.

Bioinformatic analysis revealed that all suppressor proteins consist of more basic amino acid residues then acidic amino acid. AV2 protein has more hydrophobic amino acid residues.

All suppressor proteins consist of kinase motif indicated that these proteins are activated by phosphorylation. Sub-cellular localization assay through confocal microscopy indicated that while AV2 located in cell membrane and nucleus; AC2 located in nucleus and AC4 located in cell membrane. All the suppressor proteins act as pathogenicity determinant, and AV2 showed more virulence than others. First hairpin RNAi constructs against all the suppressor genes developed through GoldenGate technology.

These RNAi constructs could effectively reduce the viral load and symptoms significantly when used as a prophylactic measure.

The molecular characterization of Fusarium fujikuroi by sequence analysis of Tef1ά, Beta tubulin, Calmodulin, RPB2, Intergenic spacer sequence (IGS) and Histone H3 revealed high polymorphism suggestive of high diversity.  

The PCR primers designed from NRPS31 region were found specific to Fusarium fujikuroi with good sensitivity indicating their potential for field detection by Loop mediated isothermal amplification PCR technique.

The transcriptional responses of defence genes in the MLB resistant and susceptible maize inbred lines viz., SC-7 and CM 119 was deciphered.  

Enhanced expression of the pathogenesis related (PR) protein and phenylalanine ammonia lyase (PAL) enzyme at different time points in resistant lines indicated their association with infection stages of B. maydis and response of the resistant line against disease establishment.  

Down regulated gene expression of pheophytinase suggests reduced enzyme activity linked with less chlorophyll degradation in the resistant line compared to the susceptible line and it could be directly correlated with symptom development of MLB disease.

The transcriptional responses of tomato to Chaetomium globosum was analysed to decipher mechanism of early blight disease suppression. The transcriptome data revealed 922 expressed genes with significant alterations. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis conformed genes associated to metabolic pathways, biosynthesis of secondary metabolites, plant–pathogen interaction, chlorophyll metabolism, and plant hormone signal transduction among the DEGs.  

The analysis further indicated active participation of jasmonic acid (JA) and salicylic acid (SA) signal transduction pathways suggestive of i induced systemic resistance (ISR) and systemic acquired resistance (SAR) in tomato.

A total of 740 whitefly samples representing Delhi, Rajasthan, Delhi, Indore and Coimbatore were subjected to molecular identification and detection of secondary endosymbionts.  

Sequencing of mitochondrial cytochrome oxidase-I gene revealed the existence of whitefly population belong to belongs to Asia-II1 genotype (Rajasthan, Indore and Coimbatore) and Asia-II7 (Delhi).  

Bacteria such as Portiera, Rickettsia and Arsenophonus were highly prevalent in all populations, while expected Cardinium was not found in all collected populations.  

The fluorescence in situ hybridization analysis showed that Hamiltonella and Portiera were localized inside the bacteriome. A FISH analysis of B. tabaci gut, nymphs and adults revealed a unique concentration of Rickettsia around the gut and follicle cells, as well as a random distribution in the hemolymph.

Cheilomenes sexmaculata representing North (Delhi, Haryana etc.,), Central (Nagpur, Akola, Amaravati etc.,), East (Cooch Behar, Jorhat etc.,), West (Navsari, Anand, Junagadh etc.,) and Karnataka (Coimbatore, Bengaluru, Tumkur etc.,) subjected to molecular analysis.  

Amplicon profiling of SSR markers revealed the diverse population structure.

The majority of culturable bacteria in the gut of A. dimidiata belonged to two phyla: Firmicutes (62.5%) and Proteobacteria (37.5%).  

Forty aerobic and eleven anaerobic bacterial strains were isolated and tested for cellulolytic, lipolytic and nitrate reductase activity, and twenty seven and thirty one cellulolytic and lipolytic gut bacteria were identified.  

The 19 isolates exhibiting both activities whereas ten facultative anaerobic bacteria isolates were positive for nitrate reductase activity.

The molecular phylogenetic analysis of the delphacid planthoppers of India was performed. Total 40 taxa comprising of 4 gene sets (28S region D2 & D9-D10, mtCOI and Histone) were used for the exploration and placement of our studied specimen. The taxon sample included the 30 species from tribe Delphacini and 9 species from tribe Trophidocephalini. Cixius scrupeus was used as only outgroup for the current analysis.  

The study showed that, both the tribe Delphacini and Trophidocephalini are bifurcated into two clear clades and supporting both the tribe as paraphyletic in nature. Also, identified a second species of Eoeurysa Muir, 1913 from India, the new species Eoeurysa sagittaria sp. nov., was found in Rampur, Una, Himachal Pradesh.  

Both new species are described with illustrations, and a molecular identification is given with the mtCOI gene sequence. A modified key to species of the genera is also provided. The results of our study highlight the fact that both the tribe Delphacini and Trophidocephalini are paraphyletic in nature and it is clearly resolved and supported by the data used in the study.

Whole genome sequencing of a Rice land race JBT 36/14 along with four of its mutants that showed resistance towards Meloidogyne graminicola was done through illumina platform. A total of 4,48,999 SNPs and 33,245 InDels were identified in JBT 36/14 respectively. Structural variations in mutant lines also led to identification of several unique variations compared to wild type and reference indica genome. Transcriptome analysis of resistant mutant line 9 with JBT-36/14 as control (submitted to NCBI GenBank; Bioproject PRJNA678974) led to identification of 674 differentially expressed genes with several PR protein coding genes (PR-1,PR-10, RRP-13, RGA 2 etc.) and several rice diterpenoid synthesis pathway genes coding for oryzalexin D,E, momilactone and phytocassane were being highly upregulated.  

The 45 putative effectors of M. graminicola were identified from its genome using comparative genomics tools. dsRNA for these genes has been prepared through in vitro transcription and were used for in vitro silencing (in vitro RNAi) of these genes for validating their functional roles in nematode pathogenicity of rice root knot nematode.  

Two effector genes after silencing showed reduced penetration and multiplication factor in the treated nematodes. Two rice cDNA libraries has been developed for yeast 2 hybrid assays. Interaction of Mgsp-26 with these libraries as bait was not observed as positive.

An inbred line of Heterorhabditis indica strain HV was developed. Whole genome sequencing of H. indica was carried out and its assembly resulted to 91.26 Mb in size and 10,974 protein coding genes were predicted. RNA-Sequencing de-novo transcriptome assembly resulted a total of 46,599 transcripts. Differential gene expression analysis and pathway analysis showed that immune pathways are highly expressed in Heterorhabditis nematode during biofilm formation stage of symbiosis with Photorhabdus bacteria.  

Screening for dsRNA uptake in different life stages of Heterorhabditis using the fluorescent dye FITC showed that Post-IJ recovery stage is amenable for RNAi by soaking.  Successful RNAi based gene function validation in Post-IJ recovery stage of Heterorhabditis:  RNAi of Hb-cct-2 gene produced sterile phenotype with defective gonad as compared to control. RNAI of Hb-dpy-7 and Hb-dpy-13 genes produced dumpy phenotypes with reduced lengths as compared to normal phenotype.

The transcriptome analysis showed that out of 8,681 DEGs in fungal filtrate treated C. elegans, 7,600 down- regulated, and 1,081 were up- regulated. Out of 9,587 DEGs in huperzine treated C. elegans, 7,668 transcripts were down- regulated, and 1,899 were up- regulated. Out of 1,635 DEGs in fungal filtrate treated M. incognita, 590 transcripts were down- regulated, and 1.045 were up- regulated. Out 979 DEGs in huperzine treated M. incognita, 597 transcripts were down- regulated, and 482 were up- regulated. These genes were found to be involved in growth, morphogenesis, cellular signalling and metabolism.