Biology subjects

Yadav, S. R.

Publications and source records attributed to Yadav, S. R..

5 recordsLinked to original sources

bioRxiv2026

Spatial Decoupling of the Endodermal Functions Establishes the Innermost Cortex as the Gravity Sensor in Rice Stems

Gravitropism is a remarkable example of coordinated growth, enabling plants to perceive gravity and generate asymmetric cell expansion that restores organ orientation. In Arabidopsis, gravity sensing in shoots occurs within starch-rich endodermis cells. In rice, however, the stem must accommodate gravitropic bending while preserving integrity of tissues surrounding emerging crown roots, raising the possibility that gravity sensing relies on distinct structural and physiological adaptations. Here, using high-resolution imaging together with auxin-response analyses, we identify a specialized cell layer at the inner boundary of the rice stem cortex, operationally defined by its position adjacent to the lignified endodermis and associated with gravitropic responses. This layer is characterized by circumferentially elongated cells, starch sedimentation, a confined auxin-response domain, and expression of gravity-sensing markers. Following gravistimulation, starch granules realign and the auxin response domain expands asymmetrically within this layer, coinciding with differential growth during stem bending. Our results further indicate that this response depends on polar auxin transport and conserved components of the gravitropic regulatory network. Together, these findings support a model in which gravity sensing and signaling in rice stems are spatially separated from the lignified endodermal barrier. Such tissue organization may represent a developmental adaptation that allows the stem to reconcile barrier integrity with growth flexibility.

plant biology↗

bioRxiv2026

Multiple evidence supporting a novel species amid complex phylogenomic discordance: a case of Indian Ledebouria based on Angiosperms353 target capture sequencing

Ledebouria, a geophytic herb native genus to Africa and represented by a few species in the Arabian Peninsula, Madagascar, India and Sri Lanka. For a long time Indian species were named as L. revoluta until recent molecular work clarified African L. revoluta is distinct from Indian and Sri Lankan species. Hence the name L. hyacinthina was resurrected. However, there is no clear molecular or morphological clarification of the different morphotypes and karyotypes observed in various accessions from peninsular India. Since plastid DNA sequence markers failed to detect diversity, we used the high density, low copy number marker set, the Angiosperms353, for phylogenomic analysis of eight accessions and analysed with the same markers from the global dataset from published work. Our analysis shows L. hyderabadensis is a distinct species, whereas other widely distributed Indian accessions under the other name L. hyacinthina are young lineages representing incipient species. Our results indicate that Ledebouria has not diversified enough at the molecular sequence level for the marker set used. The same is also true of the chloroplast sequences.

evolutionary biology↗

bioRxiv2024

Genomic sequencing and neutralizing serological profiles during acute dengue infection: A 2017 cohort study in Nepal

Dengue virus (DENV) is a mosquito-borne flavivirus that poses a threat to nearly 50% of the global population. DENV has been endemic in Nepal since 2006; however, little is known about how DENV is evolving or the prevalence of anti-DENV immunity within the Nepalese population. To begin to address these gaps, we performed a serologic and genetic study of 49 patients from across Nepal who presented at central hospitals during the 2017 dengue season with suspected DENV infection. Of the 49 subjects assessed, 21 (43%) were positive for DENV NS1 antigen; of these; 5 were also anti-DENV IgM+ IgG+; 7 were DENV IgM+ IgG-, 2 were IgM- IgG+, and 7 were IgM- IgG- by specific ELISAs. Seven of the 21 NS1+ sera were RNA+ by RT-PCR (six DENV2, one DENV3), suggesting that DENV2 was the dominant serotype in our cohort. Whole-genome sequencing of two DENV2 isolates showed similarity with strains circulating in Singapore in 2016, and the envelope genes were also similar to strains circulating in India in 2017. DENV-neutralizing antibodies (nAbs) were present in 31 of 47 sera tested (66%); among these, 20, 24, 26, and 12 sera contained nAbs against DENV1, 2, 3, and 4 serotypes, respectively. Serology analysis suggested that 12 (26%) and 19 (40%) of the 49 subjects were experiencing primary and secondary DENV infections, respectively. Collectively, our results provide evidence for current and/or past exposure to multiple DENV serotypes in our cohort, and the RNA analyses further indicate that DENV2 was the likely dominant serotype circulating in Nepal in 2017. These data suggest that expanded local surveillance of circulating DENV genotypes and population immunity will be important to effectively manage and mitigate future dengue outbreaks in Nepal.

genomics↗

bioRxiv2021

Auxin-responsive (phospho)proteome analysis reveals regulation of cell cycle and ethylene signaling during rice crown root development

The rice root system, which primarily consists of adventitious/crown roots (AR/CR) developed from the coleoptile base, is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance, and protein phosphorylation in response to an auxin stimulus during CR development. Global proteome and metabolome analyses of developing crown root primordia (CRP) and emerged CRs uncovered that the biological processes associated with chromatin conformational change, gene expression, and cell cycle were translationally regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory feedback module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Ethylene signaling promotes CR formation by repressing the cytokinin response regulator, OsRR2. Additionally, the (phospho)proteome analysis identified differential phosphorylation of the Cyclin-dependent kinase G-2 (OsCDKG;2), and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation, and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CRP trans-differentiation downstream of the auxin signaling pathway. HighlightGlobal (phospho)proteome and metabolic profiling of rice CRP and CRs uncover differential proteins and metabolites associated with gene expression, cell cycle, ethylene signaling and cell wall synthesis during CR development.

plant biology↗

bioRxiv2020

Genome-Wide High Resolution Expression Map and Functions of Key Cell Fate Determinants Reveal the Dynamics of Crown Root Development in Rice

Shoot borne adventitious/crown roots (AR/CR) shape up the root architecture in grasses. Mechanisms underlying initiation and subsequent outgrowth of CR remain largely unknown. Here, we provide genome-wide modulation in the landscape of transcriptional signatures during distinct developmental stages of CR formation in highly derived grass species, rice. Our studies implicate the role of potential epigenetic modifiers, transcription factors and cell division regulators in priming the initiation of CR primordia followed by progressive activation of conserved transcription regulatory modules to ensure their outgrowth. In depth analysis of spatio-temporal expression patterns of key cell fate determinants and functional analyses of rice WUSCHEL RELATED HOMEOBOX10 (OsWOX10) and PLETHORA (OsPLT1) genes reveal their unprecedented role in controlling root architecture. We further show that OsPLT1 activates local auxin biosynthesis and forms an integral part of ERF3-OsWOX11-OsRR2 regulatory module during CR primordia development. Interestingly, OsPLT genes, when expressed in the transcriptional domain of root-borne lateral root primordia of Arabidopsis plt mutant, rescued their outgrowth demonstrating the conserved role of PLT genes in root primordia outgrowth irrespective of their developmental origin. Together, these findings unveil the molecular framework of cellular reprogramming during trans-differentiation of shoot tissue to root leading to culmination of robust root architecture in grass species which got evolutionary diverged from dicots.

plant biology↗