De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance

Abstract

Abiotic stresses, especially drought stress, are responsible for heavy losses in productivity, which in turn poses an imminent threat for future food security. Understanding plants’ response to abiotic stress at the molecular level is crucially important for mitigating the impacts of climate change. Moringa oleifera is an important multipurpose plant with medicinal and nutritional properties and with an ability to grow in low water conditions, which makes the species an ideal candidate to study the regulatory mechanisms that modulate drought tolerance and its possible use in agroforestry system. In the present communication, we report whole-genome sequencing (WGS) of this species and assemble about 90% of the genome of M. oleifera var. Bhagya into 915 contigs with a N50 value of 4.7 Mb and predicted 32,062 putative protein-coding genes. After annotating the genome, we have chosen to study the heat shock transcription factor (HSF) family of genes to analyze their role in drought tolerance in M. oleifera. We predicted a total of 21 HSFs in the M. oleifera genome and carried out phylogenetic analyses, motif identification, analysis of gene duplication events, and differential expression of the HSF-coding genes in M. oleifera. Our analysis reveals that members of the HSF family have an important role in the plant’s response to abiotic stress and are viable candidates for further characterization.

Endophytic Fungal Consortia Enhance Basal Drought-Tolerance in Moringa oleifera by Upregulating the Antioxidant Enzyme (APX) through Heat Shock Factors

“…For exploring and elucidating the molecular mechanisms of stress resistance, the higher quality of the genome assemblies of significant plants has been prioritized by scientists for extracting the valued genomic entities, as, genomes and transcriptomics can provide vital resources to aid crop modification. [ 21 ] have recently performed genome assembly of M. oleifera var. Bhagya uses long reads (PacBio) and short reads (Illumina) to generate better genome coverage.…”

“…Expression analysis of selected HSFs and APX genes was performed as described [ 26 ]. The expression was normalized with the housekeeping gene actin as mentioned earlier [ 21 ], for the stable expression under drought stress in M. oleifera . Primer sequences have been given in Supplementary Table S2 .…”

“…More recently, whole-genome sequencing (WGS) of M. oleifera has been performed that aided the identification of several ion channel transporters, chaperons, penta-tricopeptide proteins, and various transcription factors ( HSFs , WRKY , and CCCH zinc finger) important for the survival of plants under stress. qRT-PCR also confirmed that MolHSF-8 upregulated in the M. oleifera roots the first tissue that senses drought stress to respond faster, signifying a critical regulatory role during drought stress [ 21 ]. HSFs participate to control the response to several other stresses as well, including cold, heat, and salinity [ 22 ].…”

De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal

“…The method described by Shyamli et al, 2021 [ 12 ] was used to prepare libraries. Briefly, total RNA was extracted from 100mg of frozen plant tissues using Nucleospin Plant and Fungi RNA extraction kit (REF 740120.50, Macherey-Nagel, Düren, Germany) following the manufacturer’s protocol.…”

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

“…Comparison of assembly statistics between the current moringa genome assembly using long reads (African Orphan Crops Consortium [AOCC] v2), the previous AOCC v1,and Shyamli et al (2021) …”