Biology subjects

Pantha, P.

Publications and source records attributed to Pantha, P..

6 recordsLinked to original sources

bioRxiv2026

Comparative genomics reveals potential mechanisms of invasion in Phragmites australis (common reed)

Biological invasions are transforming ecosystems worldwide, yet the genomic bases enabling certain species to dominate new environments remain poorly understood. Phragmites australis, a widespread wetland grass with invasive and native subspecies co-occurring in North America, provides a powerful system to investigate genomic mechanisms of invasiveness. We generated independent chromosome-scale genome assemblies for invasive P. australis ssp. australis and co-occurring native ssp. americanus and used comparative genomic and transcriptomic analyses to identify lineage-specific innovations associated with invasive success. The invasive subspecies exhibits genomic novelties through functionally-biased single-copy orthologs, intronless genes, and subgenome expression asymmetry, along with a stress-ready basal transcriptome relative to the native subspecies. Following the removal of aboveground shoots ("cutback"), which measures the ability to recover from damage, the invasive subspecies undergoes stronger transcriptional reprogramming, increased shoot production, and higher biomass accumulation compared to the native. It also displays expansion of gene families and coordinately expressed gene modules that support resource mobilization, growth responses to light, and stress tolerance. Beyond Phragmites, comparative analyses across multiple grass genomes, including eight invasive species with related non-invasive species, revealed repeated expansion of gene families associated with abiotic stress tolerance and developmental regulation, suggesting convergent adaptive strategies in the grass family for invasive success. Together, these results demonstrate genomic architecture linked to invasion success and highlight potential targets for managing invasive grasses.

Plant Biology↗

bioRxiv2022

Spatiotemporal gene expression atlas of the extremophyte Schrenkiella parvula

Extremophytes are naturally selected to survive environmental stresses, but scarcity of genetic resources for them developed with spatiotemporal resolution limit their use in stress biology. Schrenkiella parvula is one of the leading extremophyte models with initial molecular genomic resources developed to study its tolerance mechanisms to high salinity. Here we present a transcriptome atlas for S. parvula with subsequent analyses to highlight its diverse gene expression networks associated with salt responses. We included spatiotemporal expression profiles, expression specificity of each gene, and co-expression and functional gene networks representing 115 transcriptomes sequenced from 35 tissue and developmental stages examining their responses before and after 27 salt treatments in our current study. The highest number of tissue-preferentially expressed genes were found in seeds and siliques while genes in seedlings showed the broadest expression profiles among developmental stages. Seedlings had the highest magnitude of overall transcriptomic responses to salinity compared to mature tissues and developmental stages. Differentially expressed genes in response to salt were largely mutually exclusive but shared common stress response pathways spanning across tissues and developmental stages. Our foundational dataset created for S. parvula representing a stress-adapted wild plant lays the groundwork for future functional, comparative, and evolutionary studies using extremophytes aiming to uncover novel stress tolerant mechanisms. SIGNIFICANCE STATEMENTConcerted transcriptomic responses coordinated across developmental stages and tissues are required to complete a plant lifecycle under salt stress. Transcriptomic resources created with spatiotemporal resolution for plants are rare and for stress-adapted plants rarer. We present a transcriptome atlas enabling discovery of genes and networks evolved as adaptations to salt stress in a model extremophyte, Schrenkiella parvula. The spatiotemporally resolved gene expression networks are largely non-overlapping but functionally connected through synergistic stress responsive pathways.

plant biology↗

bioRxiv2021

Balancing growth amidst salinity stress-lifestyle perspectives from the extremophyte model Schrenkiella parvula

Schrenkiella parvula, a leading extremophyte model in Brassicaceae, can grow and complete its life cycle under multiple environmental stresses, including high salinity. While foundational genomic resources have been created for S. parvula, a comprehensive physiological or structural characterization of its salt stress responses is absent. We aimed to identify the influential traits that lead to stress-resilient growth of this species. We examined salt-induced changes in the physiology and anatomy of S. parvula throughout its lifecycle across multiple tissues. We found that S. parvula maintains or even exhibits enhanced growth during various developmental stages at salt stress levels known to inhibit growth in Arabidopsis and most crops. The resilient growth of S. parvula was associated with key traits that synergistically allow continued primary root growth, expansion of xylem vessels across the root-shoot continuum, and a high capacity to maintain tissue water levels by developing larger and thicker leaves while facilitating continued photosynthesis during salt stress. These traits at the vegetative phase were followed by a successful transition to the reproductive phase via early flowering, development of larger siliques, and production of viable seeds during salt stress. Additionally, the success of self-fertilization during early flowering stages was dependent on salt-induced filament elongation in flowers that aborted in the absence of salt. Our results suggest that the maintenance of leaf water status and enhancement of selfing in early flowers to ensure reproductive success, are among the most influential traits that contribute to the extremophyte lifestyle of S. parvula in its natural habitat. One sentence summarySchrenkiella parvula salt-resilient growth is facilitated by uncompromised primary root growth, expansion of xylem vessels, maintenance of leaf water status and photosynthesis, and early flowering.

plant biology↗

bioRxiv2021

Living with high potassium: an asset or a hindrance

O_LIHigh potassium (K) in the growth medium is more toxic to plants than Na at similar concentrations. However, the molecular mechanisms underlying plant responses to K-induced salt stress are virtually unknown. C_LIO_LIWe examined Arabidopsis thaliana and its extremophyte relative Schrenkiella parvula, using a comparative multi-omics approach to identify cellular processes affected by excess K and understand which deterministic regulatory pathways are active to avoid tissue damage while sustaining growth. C_LIO_LIA. thaliana showed limited capacity to curb excess K accumulation and prevent nutrient depletion contrasting to S. parvula which could limit excess K accumulation without restricting nutrient uptake. Facilitated by a targeted transcriptomic response, promoting nitrogen uptake along with other key nutrients and uninterrupted N assimilation into primary metabolites during excess K-stress allowed S. parvula to boost its antioxidant and osmolyte pools concurrently leading to sustained growth. Antithetically, A. thaliana showed transcriptional responses indicative of a poor balance between stress signaling, increased ROS levels, and reduced photosynthesis, subsequently leading to inhibited growth. C_LIO_LIThe ability to regulate independent nutrient uptake and a coordinated transcriptomic response to avoid non-specific stress signaling are two main deterministic steps towards building stress resilience to excess K+-induced salt stress. C_LI

plant biology↗

bioRxiv2020

A tale of two transcriptomic responses in agricultural pests via host defenses and viral replication

BackgroundAutographa californica Multiple Nucleopolyhedrovirus (AcMNPV) is a baculovirus with a high potential for its use as a biopesticide against arthropod pests. The budded form of the virus causes a systemic infection when it escapes the midgut to enter the hemolymph of susceptible hosts. Yet, the specific molecular processes underlying the biocidal activity of AcMNPV on its insect hosts are largely unknown. ResultsIn this study, we describe the transcriptional responses in two major pests, Spodoptera frugiperda and Trichoplusia ni, to determine the host-pathogen responses during AcMNPV infection, concurrently with the viral response to the host. We assembled species-specific de novo reference transcriptomes of the hemolymph to identify key transcripts that respond during pathogenesis in these arthropod models where genomic resources are sparse. We found that the suppression of transcriptional processes related to chitin, a metabolite critical for basement membrane stability and tracheal development are central in establishing a systemic infection. Synergistic transcriptional support was observed to suggest suppression of immune responses and induction of oxidative stress indicating disease progression in the host. The entire AcMNPV core genome was expressed in the host hemolymph and viral genes predominantly associated with the budded virus replication, structure, and movement were more abundant than those associated with the occlusion-derived virus. Genes known to directly arrest host cell cycle and development were among the most abundant AcMNPV transcripts in infected hosts. Interestingly, several of the host genes (e.g. Chitin synthase) that were targeted by the pathogen as revealed by our study are also targets of several chemical insecticides currently used commercially to control arthropod pests. ConclusionsOur results reveal an extensive overlap between biological processes represented by genes differently expressed in both hosts, as well as convergence on highly abundant viral genes expressed in the two hosts, providing an overview of the host-pathogen transcriptomic landscape during systemic infection. Given the diversity of AcMNPV strains that infect a wide range of insect hosts, our study provides a framework where pathogen strains could be selected to target specific host genes that facilitates modulation of the infection strength and specificity of the susceptible hosts.

genomics↗

bioRxiv2019

A RETINOBLASTOMA-RELATED transcription factor network governs egg cell differentiation and stress response in Arabidopsis

The multicellular embryo, and ultimately the entire organism, is a derivative of the fertilized egg cell. Unlike in animals, transcription factor networks orchestrating faithful egg development are still largely unknown in plants. We have identified that egg cell differentiation in Arabidopsis require interplay between evolutionarily conserved onco-protein homologs RETINOBLASTOMA-RELATED (RBR) and redundant MYB proteins MYB64/MYB119. RBR physically interacts with the MYBs; and with plant-specific transcription factors belonging to the RWP-RK-domain (RKD) family and LEAFY COTYLEDON1 (LEC1), which participate in development of egg cells and inherent stress response. RBR binds to most of these egg cell-expressed loci at the DNA level, partially overlapping with sites of histone methylation H3K27me3. Since deregulation of RKDs phenocopies mutants of RBR and the MYBs in terms of cell proliferation in the egg cell spatial domain, all the corresponding proteins are likely required to restrict parthenogenetic cell divisions of the egg cells. Cross-talk among these transcription factors, and direct regulation by RBR, govern egg cell development and expression of egg-to-zygotic polarity factors of the WUSCHEL RELATED HOMEOBOX family. Together, a network of RBR-centric transcription factors underlies egg cell development and stress response, possibly, in combination with several other predicted nodes.\n\nAuthor summaryThe RETINOBLASTOMA protein is one of the core components of the Eukaryotic cell cycle, and corresponding evolutionary homologs have been implicated not only to repress cell division but also to control differentiation and development. How RETINOBLASTOMA RELATED (RBR) associate with other higher order regulators to control faithful egg cell development in sexual plants is pivotal for manipulation of successful reproduction in general, and engineering of parthenogenesis when asexual or apomictic seed progeny are desirable over sexual plants. Using a suite of molecular methods, we show that a RBR-associated transcription factor network operates to specify egg cells in Arabidopsis. Complex cross-regulation within these transcription factors seems to be necessary for successful maternal egg cell to zygotic transition and reproductive stress response. Detailed genetic analysis implicate that RBR and its interactive partners belonging to MYB and RWP-RK transcription factor families are possibly required to prevent parthenogenesis of the sexual egg cells. Novel RBR networks and stress nodes explained in this study might help to improve our understanding of sexual and asexual reproduction.

genetics↗