Integrated mRNA and small RNA sequencing reveals post-transcriptional regulation of the sesquiterpene pathway in Santalum album L. (Indian sandalwood).

Key message: In sandalwood, negative pattern of regulation by miRNAs was documented in key genes from the sesquiterpene pathway, with cytochrome P450 reductase showing maximum miRNA targets, followed by sesquisabianene synthase 1. Abstract: A comprehensive knowledge of the molecular regulation of sesquiterpene biosynthetic pathway through transcriptomic studies is well established in Santalum album (Indian Sandalwood). However, the post-transcriptional regulation of the genes regulating the pathway is still elusive in this genus. In the present study, an integrated analysis of wood transcriptome and small RNA datasets was conducted to investigate the role of miRNAs in regulating the expression of transcripts involved in santalol production mediated by the sesquiterpene biosynthesis pathway. A total of 24,237 transcripts were annotated from the wood transcriptome, and 45 transcripts were mapped to the sesquiterpenoid pathway. Small RNA data analysis identified 257 conserved miRNAs belonging to 50 families and 7 novel putative miRNAs. Sa-miR156, Sa-miR396, Sa-miR166, and Sa-miR319 had the most number of members among the miRNA families. An integrated analysis predicted 69 miRNA members belonging to 12 families that targeted 12 transcripts from the sesquiterpene pathway, with a maximum of 24 miRNAs regulating cytochrome P450 reductase, followed by sesquisabianene synthase 1, which was targeted by 23 miRNAs. Validation of miRNA-mRNA interaction by qRT-PCR revealed a negative pattern of regulation in six miRNA-mRNA target pairs across wood tissues sourced from four genotypes. The present study provides the first crucial insight into the post-transcriptional regulation of the sesquiterpene pathway genes in the genus Santalum and opens up a new perspective in metabolite engineering for enhanced essential oil production in sandalwood. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03816-4.

The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species.

MAIN CONCLUSION: A 541 Mb draft genome of Pterocarpus santalinus is presented and evidence of whole-genome duplication in the Eocene period with expansion of drought responsive gene families is documented. Pterocarpus santalinus Linn. f., popularly known as Red Sanders, is a deciduous tree, endemic to southern parts of Eastern Ghats in India. The heartwood is highly valued in the international market due to its deep red colour, fragrant heartwood and wavy grained texture. In the present study, a high-quality draft genome of P. santalinus was assembled using short and long reads generated from Illumina and Oxford Nanopore Sequencing platforms, respectively. The haploid genome size was estimated at 541 Mb and the hybrid assembly showed 99.60% genome completeness. A total of 51,713 consensus gene set were predicted with 31,437 annotated genes. The age of the whole-genome duplication event in the species was dated at 30-39 mya with 95% confidence suggesting early genome duplication event during the Eocene period. Concurrently, phylogenomic assessment of seven Papilionoideae members including P. santalinus grouped the species based on the tribal classification and established divergence of the tribe Dalbergieae from tribe Trifolieae at ~ 54.20 mya. A significant expansion of water deprivation/drought responsive gene families documented in the study probably explains the occurrence of the species in dry rocky patches. Additionally, re-sequencing of six diverse genotypes predicted one variant every 27 bases. This report presents the first draft genome in the genus Pterocarpus and the unprecedented genomic information generated is expected to accelerate population divergence studies in the species in relation to its endemic nature, support trait-based breeding programme and aid in development of diagnostic tools for timber forensics.

Bio-prospecting of cuttle fish waste and cow dung for the production of fibrinolytic enzyme from Bacillus cereus IND5 in solid state fermentation.

The process parameters governing the production of fibrinolytic enzyme in solid state fermentation employing Bacillus cereus IND5 and using cuttle fish waste and cow dung substrate were optimized. The pH value of the medium, moisture content, sucrose, casein and magnesium sulfate were considered for two-level full factorial design and pH, casein and magnesium sulfate were identified as the important factors for fibrinolytic enzyme production. Central composite design was applied to investigate the interactive effect among variables (pH, casein and magnesium sulfate) and response surface plots were created to find the pinnacle of process response. The optimized levels of factors were pH 7.8, 1.1% casein and 0.1% magnesium sulfate. Enzyme production was increased 2.5-fold after statistical approach. The enzyme was purified up to a specific activity of 364.5 U/g proteins and its molecular weight was 47 kDa. It was stable at pH 8.0 and was highly active at 50 °C. The mixture of cuttle fish waste and cow dung could find great application as solid substrate for the production of fibrinolytic enzyme.