Biology subjects

Perumal, S.

Publications and source records attributed to Perumal, S..

11 recordsLinked to original sources

bioRxiv2026

Comparative Transcriptome Analysis Unveils Mechanisms of Salt Tolerance in Bluebunch Wheatgrass

Bluebunch wheatgrass (Pseudoroegneria spicata) exhibits substantial variation in its response to salt stress, making it a valuable model for studying salinity-tolerance mechanisms for use in crop improvement. In this study, we identified two P. spicata genotypes with contrasting responses to salt stress: the tolerant W6 56551, which maintained growth with green foliage under saline conditions, and the susceptible PI693916, which exhibited severe leaf chlorosis and stunted growth. To better understand the molecular basis of salt tolerance in blue-bunch wheatgrass, we conducted RNA-sequencing at 0, 1, and 4 days (D0, D1, and D4) after salt treatment at 160 mM level to examine changes in gene expression of salt-tolerant and salt-susceptible genotypes. Comparative analysis across time points identified 6,154 and 1,086 differentially expressed genes (DEGs) at D4 and D1 in PI693916, and 4,638 and 3,302 DEGs at D4 and D1 in W6 56551, respectively, relative to control (D0). Functional analysis of these DEGs showed that the salt-tolerant geno-type displayed an early and broad transcriptional reprogramming, including induction of photosynthesis, carbon metabolism, and flavonoid biosynthesis pathways, whereas the salt-susceptible genotype exhibited delayed and less coordinated responses, with enrichment of cyanoamino acid metabolism and repression of antioxidant-associated pathways. Notably, calcium signaling, ion transporter regulation, and osmolyte biosynthesis genes showed contrasting expression between genotypes, highlighting distinct strategies for ionic and osmotic homeostasis. Collectively, these results demonstrate that salt tolerance in P. spicata is associated with rapid metabolic adjustment, enhanced photosynthetic stability, and differential regulation of ion transport and osmoprotectant pathways.

genomics↗

bioRxiv2026

Haplotype-resolved Genome Assemblies of Hybrid Wheatgrass and Bluebunch Wheatgrass Reveal the Stepwise Polyploid Origin and Biased Subgenome Dominance

Concerns over climate change have intensified the demand for stress resistant crops like hybrid wheatgrass (HWG; Elymus hoffmannii, StStStStHH), a perennial forage species known for its exceptional salt and drought tolerance. However, hexaploidy and high heterozygosity have complicated efforts to resolve its genomic structure and evolutionary history. Here, we present high-quality, haplotype-resolved, chromosome-level genome assemblies for HWG (CDC Saltking) and its putative progenitor, bluebunch wheatgrass (Pseudoroegneria spicata, StSt). By integrating PacBio HiFi and ultra-long Oxford Nanopore sequencing with Hi-C scaffolding, we assembled the 10.7 Gb HWG genome into 21 pseudochromosomes per haplotype. Our phylogenomic analysis redefines the origin of the H subgenome, positioning it as an intermediate between Old-World Hordeum marinum (sea barley) and Hordeum brevisubulatum. Notably, we identified significant chromosomal rearrangements, including a unique duplication on St chromosome 4. Transcriptome analysis across multiple tissues revealed a pronounced expression dominance of the H subgenome. This dominance was not associated with reduced LTR density, suggesting that selective pressures for rapid adaptation of the latest subgenome entrant may drive its dominance. Finally, using the f-branch statistic, population genomic analysis of 189 accessions representing eight Elymus and Pseudoroegneria species revealed extensive reticulate evolutionary relationships and identified P. spicata as a major, asymmetric genetic donor within the wheatgrass complex. These resources provide a foundational framework for future genomic research and genetic improvement in grasses and for the introgression of stress-tolerance traits into cereal crops such as wheat. Key MessagesO_LIDevelopment of world-first high-quality chromosomal-level haplotype-resolved genome assemblies of hexaploid HWG and diploid progenitor, Pseudoroegneria spicata, enabled the identification of the subgenome origins. C_LIO_LIThis study resolved the evolutionary placement of the St genome and clarified the history of polyploidization and hybridization in HWG. C_LIO_LIHomeolog expression bias in the H subgenome likely reflects selective pressure favoring greater gene retention and upregulation of functionally important genes, thereby enhancing hybrid fitness. C_LIO_LIPopulation structure analysis distinctly differentiates P. spicata, E. repens, E. hoffmannii from other European Pseudoroegneria species. C_LIO_LIThe findings reveal the complex patterns of interspecific gene flow and population dynamics within the Elymus and Pseudoroegneria species. C_LI

genomics↗

bioRxiv2026

High-quality genome assemblies of diploid Bromus species enhance understanding of genome complexity and uncover large DNA satellite structures.

Genus Bromus includes important cool-season forage grasses, but large genome sizes and complex ploidy hinder genomic studies. Here we carried out long read sequencing of two diploid genomes, Bromus riparius and Bromus squarrosus, generating highly contiguous assemblies with contig N50 values of 294.76 Mb and 98.78 Mb, respectively. These assemblies uncovered high-order centromeric repeats and two unique large sub-telomeric repeats on chromosome 5 and 7. Repeat expansion in Bromus appears relatively recent compared to speciation events ([~]9.75 million years ago); yet strong synteny persists across species. Transposable elements such as Angela, SIRE, Athila, CRM, and Retand were identified as major contributors to genome expansion in related Bromus species. Population structure analysis resolved six major subpopulations, with wild relatives exhibiting a higher genetic divergence than cultivated types. Hybrid bromegrass lines showed a higher proportion of genomic contribution from B. inermis than B. riparius. Together, these genomic resources provide a foundation for investigating traits of interest and advancing bromegrass breeding.

genomics↗

bioRxiv2025

COMPARATIVE METAGENOMIC ASSESSMENT OF SHORT- AND LONG-READ SEQUENCING TECHNOLOGIES REVEALS UNKNOWN MICROBIAL INFORMATION IN A COMPLEX ENVIRONMENTAL SAMPLE

Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina short-read library kits at 2x150 bp and 2x250 bp read lengths alongside PacBio HiFi long-read sequencing using a complex environmental sample. Longer short reads (2x250 bp) combined with optimal library preparation approaches notably improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results similar to those of long-read sequencing. Although long reads yield more contiguous and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating the importance of strategic selection of library preparation chemistry and sequencing parameters in revealing unknown microbial information in complex biomes without requiring additional sequencing depth. IMPORTANCEMetagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2x150 bp and 2x250 bp across multiple library preparation kits, alongside PacBio long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. Optimized short-read sequencing at 2x250 bp recovered high-quality MAGs approaching those obtained with long-read technologies while substantially improving protein discovery compared to 2x150 bp at the same sequencing depth. Together, these results provide actionable guidance for experimental design and reveal how sequencing read length can be leveraged to improve the recovery of microbial and functional diversity in complex biomes.

genomics↗

bioRxiv2025

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity

Camelina sativa is an oilseed of the Brassicaceae, whose close relatives vary in ploidy number, providing a novel platform for studying plant genome evolution. The availability of diploid, tetraploid and hexaploid species of Camelina allow the evolutionary trajectory and fate of duplicated genes in the neopolyploid Camelina species to be elucidated. Here we report an improved assembly of the widely used C. sativa reference DH55 and three new genome assemblies of Camelina microcarpa; one tetraploid CN119243 (2n = 26), and two hexaploids with divergent chromosome numbers, Type 1 - CN119205 (2n=40) and Type 2 - CN120025 (2n=38). The tetraploid represents the first step in the evolutionary path to form C. sativa, while the hexaploids suggest three divergent lineages in the formation of higher ploidy Camelina species. The previously uncharacterized fourth subgenome found in C. microcarpa Type 2, although showing some homology to the C. sativa diploid progenitor genome, C. neglecta, showed numerous unique chromosomal rearrangements differentiating it from other subgenomes present in known Camelina species. Although this species was recently formed, the second subgenome showed gene expression dominance, which was in contrast to both 2n=40 Camelina species where the third subgenome was dominant. The expression dominance in Type 2 C. microcarpa contradicted the accepted two-step evolutionary process which led to the generation of related Brassicaceae species. However, the observed genome dominance in all Camelina species was negatively correlated with inter-subgenome chromatin interaction frequencies, suggesting that chromosome confirmation and proximity in the nucleus contributes to this mechanism of genome evolution. Despite the differences in genome structure, successful inter-specific hybridization provided evidence of chromosomal exchange between the divergent third sub-genomes of C. sativa and C. microcarpa Type 2, opening up a novel avenue to new diversity in the established oilseed. Key pointsO_LIAn improved genomic understanding of Camelina species and identification of distinct subgenome structures and relationships, which will facilitate strategies to increase the genetic diversity in C. sativa. C_LIO_LISubgenome evolution and subgenome dominance in polyploids is associated with chromosomal architecture and proximity in the nucleus. C_LIO_LIGenome assemblies representing all ploidy levels in the Camelina genus provide a unique and valuable platform for polyploid research. C_LI

genomics↗

bioRxiv2025

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

Bluebunch wheatgrass (BBWG: Pseudoroegneria species) is an outcrossing perennial grass of considerable ecological and agricultural importance due to its resilience in adverse environmental conditions. To gain a deeper understanding of the diversity, population structure, and genetic relationship within the Pseudoroegneria genus, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Our results identify six distinct genetic clusters, with P. spicata (a North America species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutional history of Eurasian BBWG species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, which revealed potential gene flow events. Our findings suggest that the Eurasian BBWG species have undergone reticulate evolution, characterized by substantial gene flow.

genomics↗

bioRxiv2024

In vitro anti cancer, anti inflammatory and anti oxidant activity of Celery oil (Apium graveolens)-Myristic acid based microemulsion system: Characterization and Biomedical application

Plant based compounds are frequently modified, developed into drug components to treat different types of cancer. Celery is one of the most used ingredients in daily life, exhibits potential medicinal properties and myristic acid exhibits anti microbial and inflammatory properties making it ideal candidate for combinational therapy. This study demonstrates the formulation of celery oil-myristic acid based microemulsion system with sequence of weight/volume of components to optimize stable microemulsion. the sequence of formulations were performed, optimized through pseudo ternary phase diagram and stability analysis, of which CMA ME 4 formulation were observed to transparent and stable. This CMA ME 4 was analyzed using DLS for particle size which is found to be 14.0{+/-}27.1 and PDI 0.34{+/-}0.46 through 5th day to 30th day. In vitro drug release study has been performed with stimulated physiological condition (pH 5.6) and stimulated tumor tissue (pH 7.4), the microemulsion was withdrawn in time intervals and the kinetic model is constructed to detect the behaviour of the drug release profile. Further, anti inflammatory, anti diabetic and anti obesity assays were performed to analyse the potentiality of CMA ME 4 microemulsion formulation, where the results exhibited from 80 to 90% radical scavenging and inhibition compared with the synthetic drugs. A good cytotoxic activity of CMA ME 4 microemulsion was determined by positive results of the MTT assay performed with HeLa with 80 to 90% cell death, MCF7 with 80 to 90% cell death and HUVECs was used to determine the toxicity level when the microemulsion interacts with the normal cell which is found to be 80 to 90% cell viability over time. These findings more suitably suggest that combination of natural oil with synthetic components can be effective in treatment against diseases.

pharmacology and toxicology↗

bioRxiv2024

Harnessing genome prediction in Brassica napus through a nested association mapping population

Genome prediction (GP) significantly enhances genetic gain by improving selection efficiency and shortening crop breeding cycles. Using a nested association mapping (NAM) population a set of diverse scenarios were assessed to evaluate GP for vital agronomic traits in B. napus. GP accuracy was examined by employing different models, marker sets, population sizes, marker densities, and incorporating genome-wide association (GWAS) markers. Eight models, including linear and semi-parametric approaches, were tested. The choice of model minimally impacted GP accuracy across traits. Notably, two models, rrBLUP and RKHS, consistently yielded the highest prediction accuracies. Employing a training population of 1500 lines or more resulted in increased prediction accuracies. Inclusion of single nucleotide absence polymorphism (SNaP) markers significantly improved prediction accuracy, with gains of up to 15%. Utilizing the Brassica 60K Illumina SNP array, our study effectively revealed the genetic potential of the B. napus NAM panel. It provided estimates of genomic predictions for crucial agronomic traits through varied prediction scenarios, shedding light on achievable genetic gains. These insights, coupled with marker application, can advance the breeding cycle acceleration in B. napus. Core ideasO_LIGenome prediction (GP) enhances genetic gains by improving selection efficiency and shortening breeding cycles. C_LIO_LIFactors influencing GP accuracy include model choice, marker types, and population size. C_LIO_LIInclusion of SNaP markers and highly significant GWAS markers improves prediction accuracy, shedding light on achievable genetic gains. C_LI Plain SummaryGenome prediction (GP) is a powerful tool that helps us improve crops more efficiently. In this study, we assessed how well GP works for predicting important traits in Brassica napus plants. We tested different models and marker sets to see which ones were most accurate. We found that two models, rrBLUP and RKHS, were consistently the best. Also, including certain types of genetic markers, like SNaP markers and highly significant GWAS markers, improved the predictions. Overall, our study shows that GP can help us understand the genetic potential of B. napus plants and improve breeding strategies, which can be exploited to develop better varieties more quickly, which is good news for farmers and the food supply.

genomics↗

bioRxiv2024

Molecular characterization and culture optimization of marine copepod Oithona dissimilis (Landberg, 1940) from Nagore coastal waters, Southern India

This study focused on identifying the cyclopoid copepod Oithona dissimilis found in the Nagore coastal waters of Southern India. Based on both morphological and molecular approaches to identify this species. Morphological characters were confirmed by examining the arrangement of setae and spines on the exopod of swimming legs 1-4. Molecular studies were performed using the CO 1 gene, which proved an effective marker for species identification. After identifying the Oithona dissimilis, reared them under laboratory conditions to determine the effects of various environmental parameters on their survival, nauplii production, and population density. Tested different temperatures, light intensity, pH, salinity, and diets and found that the optimum conditions for rearing Oithona dissimilis under laboratory conditions were a salinity of 25 PSU, a temperature range of 24-28{degrees} C, pH of 8, light intensity of 500 lux, and a mixed algal diet at a concentration of 30,000 cells/ml. The present study confirms the importance of accurate taxonomic identification for the Oithona group at the species level. Additionally, our findings show that rearing cyclopoid copepods under laboratory conditions that mimic their natural range of environmental parameters is crucial for the thriving culture of these organisms, the aquaculture industry frequently utilizes this as a live feed. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/580272v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@ecae13org.highwire.dtl.DTLVardef@987662org.highwire.dtl.DTLVardef@1844230org.highwire.dtl.DTLVardef@158e4d_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2021

A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is maintained in xBrassicoraphanus. B. rapa-originated transposable elements were transcriptionally silenced in xBrassicoraphanus, rendered by gain of CHG methylation in trans via small RNAs derived from the same sequences of R. sativus subgenome. Our work proposes that not only transcription compatibility but also a certain extent of genome divergence supports hybrid genome stabilization, which may explain great diversification and expansion of angiosperms during evolution.

plant biology↗

bioRxiv2020

High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome.

High-quality nanopore genome assemblies were generated for two Brassica nigra genotypes (Ni100 and CN115125); a member of the agronomically important Brassica species. The N50 contig length for the two assemblies were 17.1 Mb (58 contigs) and 0.29 Mb (963 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short read assembly for Ni100 corroborated genome integrity and quantified sequence related error rates (0.002%). The contiguity and coverage allowed unprecedented access to low complexity regions of the genome. Pericentromeric regions and coincidence of hypo-methylation enabled localization of active centromeres and identified a novel centromere-associated ALE class I element which appears to have proliferated through relatively recent nested transposition events (<1 million years ago). Computational abstraction was used to define a post-triplication Brassica specific ancestral genome and to calculate the extensive rearrangements that define the genomic distance separating B. nigra from its diploid relatives.

genomics↗