Biology subjects

Bisht, M. S.

Publications and source records attributed to Bisht, M. S..

6 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assembly of Tamarindus indica

Tamarindus indica is the sole member of the genus Tamarindus of the Leguminosae family. It is a multipurpose horticultural plant, with every part of the plant finding importance in food, medicine, and other industries. To gain an understanding of genome structure and evolution, we reported the first high-quality genome assembly of T. indica anchored to 12 chromosomes with N50 of [~]56 Mb. Supported by comprehensive transcriptome data, we reported >48,000 protein-coding genes. Through phylogenetic and evolutionary analysis, we uncovered an independent whole-genome duplication event in T. indica and highlighted the expression divergence of segmentally duplicated genes and their role in the better adaptivity of the plant. Our study thus provides first insights into its genomic organization, evolutionary history, and WGD event and thus becomes an important resource for future genetic and biotechnological studies to understand essential pathways and assist breeding programs for trait enhancements.

genomics↗

bioRxiv2024

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 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, whereas ASTRAL gene trees showed discordance due to incomplete lineage sorting (ILS). 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 adaptative 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.

genomics↗

bioRxiv2023

Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome, which is the largest genome sequenced for the first time from the worlds largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

genomics↗

bioRxiv2023

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

Phyllanthus emblica or Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position of P. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.

genomics↗

bioRxiv2022

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Bos indicus is a domestic cattle species with many indigenous breeds found in India and is important for dairy, draught work, and other household activities. Distinct phenotypic differences are observed among the breeds of this species; however, their whole genome sequences were not available. Therefore, in this study, we performed the whole genome sequencing using Illumina short-read technology to construct draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur, of which Vechur is known as the smallest cow of the world. We also report the first de novo genome assemblies of these native B. indicus breeds. Further, we constructed the 18S rRNA marker gene sequences of these B. indicus breeds, which were not yet known. Genomic analysis helped to identify the distinct bovine phenotypic characteristics-related and other biological process-related genes in this species compared to B. taurus, and to gain comparative genomic insights between the dwarf and non-dwarf breeds of this species.

genomics↗

bioRxiv2021

Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa trees reveal evolutionary mechanisms of longevity

Ficus benghalensis (Indian banyan tree) and Ficus religiosa (Peepal) trees are well-known for their long lifespan, traditional significance, and medicinal properties. Therefore, to understand the genomic and evolutionary aspect of these characteristics the whole genomes of these two Ficus species were sequenced using 10x Genomics and Oxford Nanopore sequencing platforms. The draft genome assemblies of F. benghalensis (392.89 Mbp genome containing 25,016 high-confidence coding genes), and F. religiosa (332.97 Mbp genome containing 23,929 high-confidence coding genes) were constructed. We also established the genome-wide phylogenetic position of the two Ficus trees with respect to 46 other Angiosperm plant species and studied the comparative population demographic history of these two species to show a population bottleneck event ~0.8 Mya for both the species. We also identified 7,468 orthogroups across 16 phylogenetically closer Eudicot plant species including F. benghalensis and F. religiosa. Comparative evolutionary analyses using these orthogroups, gene family expansion/contraction analysis, and gene duplication analysis showed adaptive evolution in genes involved in cellular pathways and mechanisms that are central to plant growth and development and provide genomic insights into longevity and ecological significance of these large woody trees.

genomics↗