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

From 'Farm to Fork': Exploring the Potential of Nutrient-Rich and Stress-Resilient Emergent Crops for Sustainable and Healthy Food in the Mediterranean Region in the Face of Climate Change Challenges

In the dynamic landscape of agriculture and food science, incorporating emergent crops appears as a pioneering solution for diversifying agriculture, unlocking possibilities for sustainable cultivation and nutritional bolstering food security, and creating economic prospects amid evolving environmental and market conditions with positive impacts on human health. This review explores the potential of utilizing emergent crops in Mediterranean environments under current climate scenarios, emphasizing the manifold benefits of agricultural and food system diversification and assessing the impact of environmental factors on their quality and consumer health. Through a deep exploration of the resilience, nutritional value, and health impacts of neglected and underutilized species (NUS) such as quinoa, amaranth, chia, moringa, buckwheat, millet, teff, hemp, or desert truffles, their capacity to thrive in the changing Mediterranean climate is highlighted, offering novel opportunities for agriculture and functional food development. By analysing how promoting agricultural diversification can enhance food system adaptability to evolving environmental conditions, fostering sustainability and resilience, we discuss recent findings that underscore the main benefits and limitations of these crops from agricultural, food science, and health perspectives, all crucial for responsible and sustainable adoption. Thus, by using a sustainable and holistic approach, this revision analyses how the integration of NUS crops into Mediterranean agrifood systems can enhance agriculture resilience and food quality addressing environmental, nutritional, biomedical, economic, and cultural dimensions, thereby mitigating the risks associated with monoculture practices and bolstering local economies and livelihoods under new climate scenarios.

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis

Introduction

The Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop.

Methods

In this study, comparative transcriptomics of two Ivy gourd cultivars namely "Arka Neelachal Kunkhi" (larger fruit size) and "Arka Neelachal Sabuja" (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers.

Results

The transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd.

Discussion

This study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya.

Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome of Moringa oleifera reveals unanticipated complexity in NUPTs´ formation

BACKGROUND

Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA.

RESULTS

Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms.

CONCLUSIONS

Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.

J, Kizhakkedath P, Mehta PA, Hariharan GN. Ajay Kumar Parida (1963-2022), an eminent plant biotechnologist with a passion for mangrove biology

We remember Dr Ajay Parida, a leading plant biotechnologist, whose premature passing has deprived the Indian plant science community of a committed scientist and an able administrator. Born on 12 December 1963 in Bhagabanpur, Cuttack District (now Jajpur district), Odisha, he passed away in Guwahati on 19 July 2022. A collegial scientist, his down-to-earth and approachable nature, as well as his resourcefulness were instrumental in advancing the cause of Indian science and harnessing frontier biotechnological tools as vehicles of social consciousness. His expertise in quantitative DNA variation and molecular marker analysis, paved the way for subsequent research on mangrove molecular diversity at the M. S. Swaminathan Research Foundation (MSSRF), Chennai. His contributions to mangrove biology, genetics and genomics as well as extremophile plant species in the Indian context over two decades are a benchmark in his field. He also provided commendable leadership in his capacity as Director, Institute of Life Sciences (ILS), Bhubaneshwar during the COVID-19 pandemic.

ACC deaminase-producing endophytic fungal consortia promotes drought stress tolerance in M.oleifera by mitigating ethylene and H2O2

INTRODUCTION

Drought has become more prevalent due to dramatic climate change worldwide. Consequently, the most compatible fungal communities collaborate to boost plant development and ecophysiological responses under environmental constraints. However, little is known about the specific interactions between non-host plants and endophytic fungal symbionts that produce growth-promoting and stress-alleviating hormones during water deficits.

METHODS

The current research was rationalized and aimed at exploring the influence of the newly isolated, drought-resistant, ACC deaminase enzyme-producing endophytic fungi Trichoderma gamsii (TP), Fusarium proliferatum (TR), and its consortium (TP+TR) from a xerophytic plant Carthamus oxycantha L. on Moringa oleifera L. grown under water deficit induced by PEG-8000 (8% osmoticum solution).

RESULTS

The current findings revealed that the co-inoculation promoted a significant enhancement in growth traits such as dry weight (217%), fresh weight (123%), root length (65%), shoot length (53%), carotenoids (87%), and chlorophyll content (76%) in comparison to control plants under water deficit. Total soluble sugars (0.56%), proteins (132%), lipids (43%), flavonoids (52%), phenols (34%), proline (55%), GA₃ (86%), IAA (35%), AsA (170%), SA (87%), were also induced, while H₂O₂ (-45%), ABA (-60%) and ACC level (-77%) was decreased by co-inoculation of TP and TR in M. oleifera plants, compared with the non-inoculated plants under water deficit. The co-inoculum (TP+TR) also induced the antioxidant potential and enzyme activities POX (325%), CAT activity (166%), and AsA (21%), along with a lesser decrease (-2%) in water potential in M. oleifera plants with co-inoculation under water deficit compared with non-inoculated control. The molecular analysis for gene expression unraveled the reduced expression of ethylene biosynthesis and signaling-related genes up to an optimal level, with an induction of antioxidant enzymatic genes by endophytic co-inoculation in M. oleifera plants under water deficit, suggesting their role in drought stress tolerance as an essential regulatory function.

CONCLUSION

The finding may alert scientists to consider the impacts of optimal reduction of ethylene and induction of antioxidant potential on drought stress tolerance in M. oleifera. Hence, the present study supports the use of compatible endophytic fungi to build a bipartite mutualistic symbiosis in M. oleifera non-host plants to mitigate the negative impacts of water scarcity in arid regions throughout the world.

Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products

Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.

Genome-Wide Identification and Expression Analysis of HSF Transcription Factors in Alfalfa (Medicago sativa) under Abiotic Stress

Alfalfa (Medicago sativa) is one of the most important legume forage species in the world. It is often affected by several abiotic stressors that result in reduced yields and poor growth. Therefore, it is crucial to study the resistance of M. sativa to abiotic stresses. Heat shock transcription factors (HSF) are key players in a number of transcriptional regulatory pathways. These pathways play an essential role in controlling how plants react to different abiotic stressors. Studies on the HSF gene family have been reported in many species but have not yet undergone a thorough analysis in M. sativa. Therefore, in order to identify a more comprehensive set of HSF genes, from the genomic data, we identified 16 members of the MsHSF gene, which were unevenly distributed over six chromosomes. We also looked at their gene architectures and protein motifs, and phylogenetic analysis allowed us to divide them into 3 groups with a total of 15 subgroups. Along with these aspects, we then examined the physicochemical properties, subcellular localization, synteny analysis, GO annotation and enrichment, and protein interaction networks of amino acids. Finally, the analysis of 16 MsHSF genes' expression levels across all tissues and under four abiotic stresses using publicly available RNA-Seq data revealed that these genes had significant tissue-specific expression. Moreover, the expression of most MsHSF genes increased dramatically under abiotic stress, further validating the critical function played by the MsHSF gene family in abiotic stress. These results provided basic information about MsHSF gene family and laid a foundation for further study on the biological role of MsHSF gene in response to stress in M. sativa.

Functional Characterization of Heat Shock Factor (CrHsf) Families Provide Comprehensive Insight into the Adaptive Mechanisms of Canavalia rosea (Sw.) DC. to Tropical Coral Islands

Heat shock transcription factors (Hsfs) are key regulators in plant heat stress response, and therefore, they play vital roles in signal transduction pathways in response to environmental stresses, as well as in plant growth and development. Canavalia rosea (Sw.) DC. is an extremophile halophyte with good adaptability to high temperature and salt-drought tolerance, and it can be used as a pioneer species for ecological reconstruction on tropical coral islands. To date, very little is known regarding the functions of Hsfs in the adaptation mechanisms of plant species with specialized habitats, especially in tropical leguminous halophytes. In this study, a genome-wide analysis was performed to identify all the Hsfs in C. rosea based on whole-genome sequencing information. The chromosomal location, protein domain or motif organization, and phylogenetic relationships of 28 CrHsfs were analyzed. Promoter analyses indicated that the expression levels of different CrHsfs were precisely regulated. The expression patterns also revealed clear transcriptional changes among different C. rosea tissues, indicating that the regulation of CrHsf expression varied among organs in a developmental or tissue-specific manner. Furthermore, the expression levels of most CrHsfs in response to environmental conditions or abiotic stresses also implied a possible positive regulatory role of this gene family under abiotic stresses, and suggested roles in adaptation to specialized habitats such as tropical coral islands. In addition, some CrHsfAs were cloned and their possible roles in abiotic stress tolerance were functionally characterized using a yeast expression system. The CrHsfAs significantly enhanced yeast survival under thermal and oxidative stress challenges. Our results contribute to a better understanding of the plant Hsf gene family and provide a basis for further study of CrHsf functions in environmental thermotolerance. Our results also provide valuable information on the evolutionary relationships among CrHsf genes and the functional characteristics of the gene family. These findings are beneficial for further research on the natural ecological adaptability of C. rosea to tropical environments.

Genomic Analysis of LEA Genes in Carica papaya and Insight into Lineage-Specific Family Evolution in Brassicales

Late embryogenesis abundant (LEA) proteins comprise a diverse superfamily involved in plant development and stress responses. This study presents a first genome-wide analysis of LEA genes in papaya (Carica papaya L., Caricaceae), an economically important tree fruit crop widely cultivated in the tropics and subtropics. A total of 28 members were identified from the papaya genome, which belong to eight families with defined Pfam domains, i.e., LEA_1 (3), LEA_2 (4), LEA_3 (5), LEA_4 (5), LEA_5 (2), LEA_6 (2), DHN (4), and SMP (3). The family numbers are comparable to those present in Ricinus communis (Euphorbiaceae, 28) and Moringa oleifera (Moringaceae, 29), but relatively less than that found in Moringa oleifera (Cleomaceae, 39) and Arabidopsis thaliana (Brassicaceae, 51), implying lineage-specific evolution in Brassicales. Indeed, best-reciprocal-hit-based sequence comparison and synteny analysis revealed the presence of 29 orthogroups, and significant gene expansion in Tarenaya and Arabidopsis was mainly contributed by whole-genome duplications that occurred sometime after their split with the papaya. Though a role of transposed duplication was also observed, tandem duplication was shown to be a key contributor in gene expansion of most species examined. Further comparative analyses of exon-intron structures and protein motifs supported fast evolution of this special superfamily, especially in Arabidopsis. Transcriptional profiling revealed diverse expression patterns of CpLEA genes over various tissues and different stages of developmental fruit. Moreover, the transcript level of most genes appeared to be significantly regulated by drought, cold, and salt stresses, corresponding to the presence of cis-acting elements associated with stress response in their promoter regions. These findings not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further functional analysis of LEA genes in papaya.

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

The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced and a first draft assembly was published in 2019. Given the extensive uses and culture of moringa, often referred to as the multipurpose tree, we generated a significantly improved new version of the genome based on long-read sequencing into 14 pseudochromosomes equivalent to n = 14 haploid chromosomes. We leveraged this nearly complete version of the moringa genome to investigate main drivers of gene family and genome evolution that may be at the origin of relevant biological innovations including agronomical favorable traits. Our results reveal that moringa has not undergone any additional whole-genome duplication (WGD) or polyploidy event beyond the gamma WGD shared by all core eudicots. Moringa duplicates retained following that ancient gamma events are also enriched for functions commonly considered as dosage balance sensitive. Furthermore, tandem duplications seem to have played a prominent role in the evolution of specific secondary metabolism pathways including those involved in the biosynthesis of bioactive glucosinolate, flavonoid, and alkaloid compounds as well as of defense response pathways and might, at least partially, explain the outstanding phenotypic plasticity attributed to this species. This study provides a genetic roadmap to guide future breeding programs in moringa, especially those aimed at improving secondary metabolism related traits.

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

Global climate change has imposed harsh environmental conditions such as drought. Naturally, the most compatible fungal consortia operate synergistically to enhance plant growth and ecophysiological responses against abiotic strains. Yet, little is known about the interactions between phytohormone-producing endophytic fungal symbionts and plant growth under drought stress. The existing research was rationalized to recognize the role of newly isolated drought-resistant, antioxidant-rich endophytic fungal consortia hosting a xerophytic plant, Carthamus oxycantha L., inoculated to Moringa oleifera L. grown under drought stress of 8% PEG (polyethylene glycol-8000). Under drought stress, the combined inoculation of endophytic strain Microdochium majus (WA), Meyerozyma guilliermondi (TG), and Aspergillus aculeatus (TL3) exhibited a significant improvement in growth attributes such as shoot fresh weight (1.71-fold), shoot length (0.86-fold), root length (0.65-fold), dry weight (2.18-fold), total chlorophyll (0.46-fold), and carotenoids (0.87-fold) in comparison to control (8% PEG). Primary and secondary metabolites were also increased in M. oleifera inoculated with endophytic consortia, under drought stress, such as proteins (1.3-fold), sugars (0.58-fold), lipids (0.41-fold), phenols (0.36-fold), flavonoids (0.52-fold), proline (0.6-fold), indole acetic acid (IAA) (4.5-fold), gibberellic acid (GA) (0.7-fold), salicylic acid (SA) (0.8-fold), ascorbic acid (ASA) (1.85-fold), while abscisic acid (ABA) level was decreased (−0.61-fold) in comparison to the control (8% PEG). Under drought stress, combined inoculation (WA, TG, TL3) also promoted the antioxidant activities of enzymes such as ascorbate peroxidase (APX) (3.5-fold), catalase (CAT) activity (1.7-fold), and increased the total antioxidant capacity (TAC) (0.78-fold) with reduced reactive oxygen species (ROS) such as H2O2 production (-0.4-fold), compared to control (8% PEG), and stomatal aperture was larger (3.5-fold) with a lesser decrease (-0.02-fold) in water potential. Moreover, combined inoculation (WA, TG, TL3) up regulated the expression of MolHSF3, MolHSF19, and MolAPX genes in M. oleifera under drought stress, compared to the control (8% PEG), is suggestive of an important regulatory role for drought stress tolerance governed by fungal endophytes. The current research supports the exploitation of the compatible endophytic fungi for establishing the tripartite mutualistic symbiosis in M. oleifera to alleviate the adverse effects of drought stress through strong antioxidant activities.

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

BACKGROUND

The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers.

RESULTS

We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis.

CONCLUSIONS

The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement.