Biotechnological interventions hold the promise for food and nutritional security and the novel biomolecules production. Bioactive compounds are natural compounds present in different crop/plants species and remarkably promote health benefits by prevention of diseases like cardiovascular disease, cancer and other diseases. Fruits, vegetables and food grains comprise of major part in balanced diet and are having significant number of bioactive molecules. Bioactive molecules present in medicinal plants are also commercially exploited at large scale by pharmaceutical based industries for plant-based drug formulations. Biotechnological applications such as plant tissue culture (conservation and propagation of valuable, rare and endangered plants), cell culture and tissue engineering (mass production of bioactive constituents via callus or suspension cultures), genetic engineering, pathway and metabolic engineering (for genetic makeup modification for higher biomass production) plays significant role high quality plant material supply and value addition to harness the potential applications. This chapter addresses the biotechnological applications of health promising bioactive molecules present in vegetable crops and medicinal herbs/plants.

Biotechnological application of health promising bioactive molecules

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

/pdf/mangrove-tree-avicennia-marina-insight-into-chloroplast-3bpsydegl6.pdf

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae.

Plants are an essential part of every food chain on earth. In addition, the humans utterly rely on plants for their every single need including food, shelter, oils, drugs, dyes, flavors, perfumes, etc. Due to the perpetually increasing population, the burden is increasing at an alarming rate. The whole scenario is worsened by changing climatic conditions, overexploitation of natural resources, and deforestation. Due to the combination of all these factors, there is a serious level of pressure which enforces stress on the plants. As a result, abiotic stresses including flooding, drought, heat shock, cold stress, etc. majority hampers crop productivity. Similar to the overall productivity of crops in the post-genomic era, the rates for various types of sequencing, MS analysis, and metabolite profiling have also fallen down. As a result, several genes, proteins, and metabolites which play role in stress tolerance have been identified and annotated. This flow of information with respect to abiotic stress research has resulted in a number of databases for different omics approaches including genomics, proteomics, miRNAomics, transcriptomics, metabolomics, etc. These various technologies provide a holistic picture of stress responses and hence provide a way to better strategies for the current situation challenges. In this book chapter, we have highlighted various useful databases available to the crop scientists and breeders.

Databases: A Weapon from the Arsenal of Bioinformatics for Plant Abiotic Stress Research

Observation rainfall networks in developing countries such as Nepal face many challenges (like availability and quality). Global Precipitation Products (GPPs) could be an alternative to gauge-based observed rainfall (GOR) in hydro-meteorological studies. However, GPPs performance across the Himalayan regions is still unknown and is influenced by several factors such as spatial and temporal resolutions, primary data sources, etc. We have comprehensively assessed the suitability of the latest GPPs using categorical and continuous variable performance metrics for the Gandak River Basin in the Nepalese Himalayas. We then ranked GPPs for the first time using the Multicriteria Decision-Making technique. 11 out of 12 GPPs considered underestimated the annual rainfall in the basin. Performance of GPPs was also inconsistent for monthly/annual and daily timescales. At longer timescales, CHIRPS and IMERG_Final are better at representing the spatial and temporal pattern of the rainfall (spatial correlation of 0.75) and least percentage bias (PBIAS < 12%). At a daily timescale, IMERG_Final, ERA5, and PERSIANN_CDR stand out for probability of detection (POD) of rainfall, while all GPPs perform poorly in false alarm ratio (FAR). Although all GPPs have relatively high RMSE (6-14 mm/day), correlation (CC) with observed rainfall was high for IMERG_Final, ERA5, and MERRA_2 in most of the sub-basins. With elevation, the performance of all GPPs is reduced, as evidenced by higher PBIAS, and lower CC. Although there is plenty of room for improvements in rainfall estimation by GPPs, among the existing dataset, IMERG_Final scored best in the majority of the performance indicators and ranked first in five out of six sub-basins. It would be relatively the better choice in the data sparse Himalayan region when daily rainfall data is required. For applications that require monthly/annual rainfall, both CHIRPS and IMERG_Final are equally suitable. The method proposed in the study for assessing GPPs can be readily applied in other river basins and at sub-daily timescales. 

/pdf/a-comprehensive-assessment-of-suitability-of-global-30vaox1b.pdf

“A comprehensive assessment of suitability of Global Precipitation Products for hydro-meteorological applications in a data-sparse Himalayan region”

Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In the present analysis, an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuatus (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.

https://horizonepublishing.com/journals/index.php/PST/article/download/697/376

Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)

Natural products are being targeted as alternative anticancer agents due to their non-toxic and safe nature. The present study was conducted to explore the in vitro anticancer potential of Justicia adhatoda (J. adhatoda) leaf extract. The methanolic leaf extract was prepared, and the phytochemicals and antioxidant potential were determined by LCMS analysis and DPPH radical scavenging assay, respectively. A docking study performed with five major alkaloidal phytoconstituents showed that they had a good binding affinity towards the active site of NF-κB. Cell viability assay was carried out in five different cell lines, and the extract exhibited the highest cytotoxicity in MCF-7, a breast cancer cell line. Extract-treated cells showed a significant increase in nitric oxide and reactive oxygen species production. Cell cycle analysis showed an arrest in cell growth at the Sub-G0 phase. The extract successfully inhibited cell migration and colony formation and altered mitochondrial membrane potential. The activities of superoxide dismutase and glutathione were also found to decrease in a dose-dependent manner. The percentage of apoptotic cells was found to increase in a dose-dependent manner in MCF-7 cells. The expressions of caspase-3, Bax, and cleaved-PARP were increased in extract-treated cells. An increase in the expression of NF-κB was found in the cytoplasm in extract-treated cells. J. adhatoda leaf extract showed a potential anticancer effect in MCF-7 cells.

/pdf/in-vitro-anticancer-activity-of-methanolic-extract-of-2xjlgvy6.pdf

In Vitro Anticancer Activity of Methanolic Extract of Justicia adhatoda Leaves with Special Emphasis on Human Breast Cancer Cell Line

Bioinformatics resources serve as an important source of data, knowledge, and information in biological studies, including plants having medicinal properties. Most of the plants found in nature have different medicinal properties; therefore, these are used to cure many human diseases from ancient times all over the world. Plant-derived medicines are an important source of lifesaving drugs. The availability of bioinformatics resources brought a major change in medicinal plant research, in terms of time, money, and labor. In this chapter, we have focused on various biological databases which are helpful in medicinal plant research and may result in a rapid and cost-effective lead generation toward finding remedies from plants.

Biological Databases for Medicinal Plant Research

Bioinformatics play an invaluable role in many areas of biological research including stress biology. In the present global scenario, almost every organism faces stress as a response to stressors (biotic or abiotic). Any stress has serious impact on the overall growth and development of organisms. Moreover, productivity of plants is also affected by stress. Due to these reasons, stress biology has been the focus of research for many scientists, and the massive data generated by them require appropriate management and analysis tools. The availability of bioinformatics tools including software, databases, and web resources has brought a major change in the stress-related research. These resources help in the analysis and better interpretation of the data generated through experiments. This chapter deals with various general and specialized bioinformatics resources useful for the stress biology community working on plants.

Bioinformatics Resources for the Stress Biology of Plants

Simple sequence repeats (SSRs) consists of 1–6 nucleotides and are widely used molecular marker. These repeats are found in almost all organisms. However, the distribution of chloroplast SSRs (cpSSRs) is not well understood in genus A rabidopsis. To annotate the current knowledge of putative polymorphic, common, and unique cpSSRs of genus Arabidopsis, a sum of 628 cpSSRs were mined. Mononucleotides (338, 53.82%) were most abundant followed by tetranucleotides (133, 21.18%), di-nucleotides (79, 12.58%), tri-nucleotides (41, 6.53%), penta-nucleotides (19, 3.03%), and hexa-nucleotide (8, 1.27%) repeats. Apart from this, 10 compound (1.60%) cpSSRs were detected. Common, unique, and polymorphic cpSSRs were also identified. Primer pairs were designed to study cross species transferability. The cpSSRs identified in this study can be helpful in species identification, genetic mapping, and diversity studies of genus Arabidopsis.

Common, Unique and Polymorphic Simple Sequence Repeats in Chloroplast Genomes of genus Arabidopsis

Computational Resources for Bryology

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