Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties

Eco-friendly N,P-CQDs from Phyllanthus emblica: A fluorescent Nanoprobe for ultra-sensitive detection of plasticizers in packaged dairy products

In this study, nitrogen- and phosphorus-co-doped carbon quantum dots (N,P-CQDs) were synthesized via a green hydrothermal method using Phyllanthus emblica for the sensitive detection of dibutyl phthalate (DBP) in plastic-packaged milk products. This research aimed to develop a sustainable, cost-effective sensing platform for monitoring food safety. The synthesized N,P-CQDs exhibited distinctive fluorescence properties with a quantum yield (QY) of 36.65 % and were characterized using high-resolution transmission electron microscopy (HR-TEM), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and UV-visible spectroscopy (UV-Vis). These N,P-CQDs showed stable fluorescence, good resistance to changes in pH, and the ability to adapt to changes in ionic strength. This made them ideal for detecting DBP in food materials. A fluorescence quenching assay revealed a broad linear response in the 1-25 μM range and achieved a low limit of detection (LOD) of 0.632 μM. Fluorescence lifetime analysis and FTIR studies confirmed a dynamic quenching mechanism driven by the inner filter effect (IFE) between DBP and N,P-CQDs. This fluorescence-based approach offers a more cost-effective, rapid, and environmentally friendly alternative than conventional DBP detection methods such as high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS). Recovery experiments conducted in spiked food matrices (milk, cheese, and yogurt) demonstrated recovery rates ranging from 97.60 % to 101.67 %, further validating the method's reliability in complex food samples. This method provides a reliable, sustainable, and cost-effective strategy for DBP detection, ensuring food safety and environmental monitoring while addressing the limitations of conventional analytical techniques.

A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop

Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution, and demographic history. The genome has a size of 730.4 Mb with an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots. Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole-genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation, and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptive evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value, and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.

Third generation sequencing transforming plant genome research: Current trends and challenges

In recent years, third-generation sequencing (TGS) technologies have transformed genomics and transcriptomics research, providing novel opportunities for significant discoveries. The long-read sequencing platforms, with their unique advantages over next-generation sequencing (NGS), including a definitive protocol, reduced operational time, and real-time sequencing, possess the potential to transform plant genomics. TGS optimizes and enhances the efficiency of data analysis by removing the necessity for time-consuming assembly tools. The current review examines the development and application of bioinformatics tools for data analysis and annotation, driven by the rapid advancement of TGS platforms like Oxford Nanopore Technologies and Pacific Biosciences. Transcriptome analysis utilizing TGS has been extensively employed to elucidate complex plant transcriptomes and genomes, particularly those characterized by high frequencies of duplicated genomes and repetitive sequences. As a result, current methodologies that allow for generating transcriptomes and comprehensive whole-genome sequences of complex plant genomes employing tailored hybrid sequencing techniques that integrate NGS and TGS technologies have been emphasized herein. This paper, thus, articulates a vision for a future in which TGS effectively addresses the challenges faced in plant research, offering a comprehensive understanding of its advantages, applications, limitations, and promising prospects.

Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'

Phyllanthus emblica L. is an edible plant with medicinal properties native to the dry-hot valley of Yunnan, China. Here, we report a de novo chromosome-scale genome of P. emblica wild type 'Yingyu'. 'Yingyu' is an octopoid plant with a total of 104 chromosomes. In total, we assembled and clustered 480 Mb of the genome and constructed 26 pseudochromosomes (haplotypes) of P. emblica wild type 'Yingyu' that encompass 97.9% of the genome and demonstrate to have relatively high integrity. We annotated 31,111 genes found in the genome of P. emblica. We screened 5 different tissues for searching the tissue-specific expression candidate genes. Four unknown function candidate genes were expressed at high levels in the flowers while genes relating to the biosynthesis of gibberellins and cellulose were specifically expressed in the fruits. The ascorbate biosynthesis-related genes were screened on P. emblica 'Yingyu' genome. The high expression level of 2 GDP-mannose epimerases and one L-galactono-1,4- lactone dehydrogenases in the fruit may be related to the activity of absorbate biosynthesis in the fruit. The chromosome-level genomic data for P. emblica we report will be important for the development of molecular markers to facilitate the selection of superior cultivars for processing and pharmaceuticals.

The complete chloroplast genome sequence of Cathetus clarkei Hook.f.1890 R.W.Bouman, 2022 (Phyllanthaceae)

Cathetus clarkei, a significant folk medicinal plant, is utilized to treat a variety of ailments. In this study, we reported the complete chloroplast genome sequence of this species. The length of the complete chloroplast genome was 155,810 bp, included a pair of inverted repeat (IR) regions (26,340 bp), a large single-copy region (LSC, 84,853 bp), and a small single-copy region (SSC, 18,277 bp). It comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total GC content was 36.8%. The phylogenetic tree revealed that C. clarkei had a close relationship with P. cochinchinensis, followed by P. reticulatus. This study provides a reference for important medicinal plants within the Phyllanthaceae, and we can gain a deeper understanding of how the species adapts to changes in the environment, helping us to identify and protect it.

Genome of the most noxious weed water hyacinth (Eichhornia crassipes) provides insights into plant invasiveness and its translational potential

The invasive character of Eichhornia crassipes (water hyacinth) is a major threat to global biodiversity and ecosystems. To investigate the genomic basis of invasiveness, we performed the genome and transcriptome sequencing of E. crassipes and reported the genome of 1.11 Gbp size with 63,299 coding genes and N50 of 1.98 Mb. We confirmed a recent whole genome duplication event in E. crassipes that resulted in high intraspecific collinearity and significant expansion in gene families. Further, the orthologs gene clustering analysis and comparative evolutionary analysis with 14 other aquatic invasive and non-invasive angiosperm species revealed adaptive evolution in genes associated with plant-pathogen interaction, hormone signaling, abiotic stress tolerance, heavy metals sequestration, photosynthesis, and cell wall biosynthesis with highly expanded gene families, which contributes toward invasive characteristics of the water hyacinth. However, these characteristics also make water hyacinth an excellent candidate for biofuel production, phytoremediation, and other translational applications.

Genome sequencing and functional analysis of a multipurpose medicinal herb Tinospora cordifolia (Giloy)

Tinospora cordifolia (Willd.) Hook.f. & Thomson, also known as Giloy, is among the most important medicinal plants that have numerous therapeutic applications in human health due to the production of a diverse array of secondary metabolites. To gain genomic insights into the medicinal properties of T. cordifolia, the genome sequencing was carried out using 10× Genomics linked read and Nanopore long-read technologies. The draft genome assembly of T. cordifolia was comprised of 1.01 Gbp, which is the genome sequenced from the plant family Menispermaceae. We also performed the genome size estimation for T. cordifolia, which was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed. The genome and transcriptome assemblies were used to construct the gene set, resulting in 17,245 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also positioned as basal eudicot by constructing a genome-wide phylogenetic tree using multiple species. Further, a comprehensive comparative evolutionary analysis of gene families contraction/expansion and multiple signatures of adaptive evolution was performed. The genes involved in benzyl iso-quinoline alkaloid, terpenoid, lignin and flavonoid biosynthesis pathways were found with signatures of adaptive evolution. These evolutionary adaptations in genes provide genomic insights into the presence of diverse medicinal properties of this plant. The genes involved in the common symbiosis signalling pathway associated with endosymbiosis (Arbuscular Mycorrhiza) were found to be adaptively evolved. The genes involved in adventitious root formation, peroxisome biogenesis, biosynthesis of phytohormones, and tolerance against abiotic and biotic stresses were also found to be adaptively evolved in T. cordifolia.