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In the study, a previously isolated plant beneficial endophytic B. cereusCaB1 was selected for the detailed analysis by whole-genome sequencing. The WGS has generated a total of 1.9 GB high-quality data which was assembled into a 5,257,162 bp genome with G + C content of 35.2%. Interestingly, CaB1 genome was identified to have 40 genes with plant beneficial functions by bioinformatic analysis. At the same time, it also showed the presence of various virulence factors except the diarrhoeal toxin, cereulide. Upon comparative analysis of CaB1 with other B. cereusstrains, it was found to have random distributions of virulence and plant growth promoting traits. The core genome phylogenetic analysis of the Bacillus cereusstrains further showed the close relation of plant associated strains with isolates from spoiled food products. The observed genome flexibility of B. cereusthus indicates its ability to make use of diverse hosts, which can result either in beneficial or harmful effects.

Plant–parasitic root-knot nematode Meloidogyne incognitauses an array of effector proteins to establish successful plant infections. Mi-msp-1and Mi-msp-20are two known effectors secreted from nematode subventral oesophageal glands; Mi-msp-1being a putative secretory venom allergen AG5-like protein, whereas Mi-msp-20is a pioneer gene with a coiled-coil motif. Expression of specific effector is known to cause disturbances in the expression of other effectors. Here, we used RNA-Seq to investigate the pleiotropic effects of silencing Mi-msp-1and Mi-msp-20. A total of 25.1–51.9 million HQ reads generated from Mi-msp-1and Mi-msp-20silenced second-stage juveniles (J2s) along with freshly hatched J2s were mapped to an already annotated M. incognitaproteome to understand the impact on various nematode pathways. As compared to control, silencing of Mi-msp-1caused differential expression of 29 transcripts, while Mi-msp-20silencing resulted in differential expression of a broader set of 409 transcripts. In the Mi-msp-1silenced J2s, cytoplasm (GO:0005737) was the most enriched gene ontology (GO) term, whereas in the Mi-msp-20silenced worms, embryo development (GO:0009792), reproduction (GO:0000003) and nematode larval development (GO:0002119) were the most enriched terms. Limited crosstalk was observed between these two effectors as a sheer 5.9% of the up-regulated transcripts were common between Mi-msp-1and Mi-msp-20silenced nematodes. Our results suggest that in addition to the direct knock-down caused by silencing of Mi-msp-1and Mi-msp-20, the cascading effect on other genes might also be contributing to a reduction in nematode's parasitic abilities.

Key message: The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanicawith pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications. Abstract: Plumbago zeylanicais a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanicausing Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 “Unigenes” transcripts with an average size of 1325 bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the “Unigenes” revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of “Unigenes” encoding enzymes of ‘Phenylpropanoid biosynthesis pathway’ represents the largest group (84 transcripts) followed by ‘Terpenoid Backbone biosynthesis’ (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate “Unigenes” transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica.Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate “Unigenes” enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.