Biology subjects

Umapathy, G.

Publications and source records attributed to Umapathy, G..

10 recordsLinked to original sources

bioRxiv2025

Nuclear and mitochondrial genome assemblies of Indrella ampulla, a terrestrial gastropod endemic to the Western Ghats

Indrella ampulla is a polymorphic, brightly coloured, forest-dwelling land snail endemic to the Western Ghats of India. Studying and understanding evolutionary processes occurring within this species has remained a challenge largely due to a paucity of genomic resources. We present high-quality annotated nuclear and mitochondrial genome assemblies of I. ampulla. The nuclear genome is assembled through a hybrid approach using Illumina short reads and Oxford Nanopore long reads, with an N50 value of 632 kb and 90.3% BUSCO genome completeness. The mitogenome is 13,887 bp long. The demographic history reconstruction based on the genomic data exhibits signatures of population decline during the last 100,000 years. This genome will aid in deciphering the colour polymorphism in I. ampulla and augmenting the general understanding of the evolution of gastropods. SignificanceIndrella ampulla is a terrestrial gastropod endemic to the Western Ghats biodiversity hotspot, and exhibits color polymorphism. The genome of I. ampulla provides a valuable resource for understanding molluscan biology, coloration genetics, adaptation, and other evolutionary processes. Our historical demographic analysis offers insights into past population dynamics of this species endemic to the Western Ghats of India, contributing to broader research on biodiversity patterns in tropical ecosystems. The bioinformatics pipeline used in this study provides a reliable framework for assembling high-quality genomes with long-read coverage as low as 10X, making it especially useful for gastropods and other species where obtaining high coverage data is a challenge. Overall, this genome will complement future studies in phylogenomics, comparative genomics, and conservation of molluscs.

genomics↗

bioRxiv2025

Cyanobacterial metagenomes reflect the spatiotemporal variations in a coastal brackish lagoon

Cyanobacteria play vital roles in aquatic ecosystems by driving photosynthesis, nitrogen fixation, carbon sequestration, and forming symbiotic relationships with diverse organisms. However, their proliferation can trigger harmful algal blooms, posing risks to aquatic biodiversity and public health. Despite their ecological significance, the interplay between cyanobacterial genomic traits and ecosystem dynamics remains poorly resolved. Here, we employed culture-independent metagenomic approaches to reconstruct cyanobacterial metagenome-assembled genomes (MAGs) from Chilika Lagoon, India, and investigate their spatiotemporal distribution and functions. Our analysis revealed distinct temporal patterns in cyanobacterial MAG abundance, with salinity emerging as the primary environmental driver of community structure and functional gene composition. Genes associated with biogeochemical cycling and toxin synthesis displayed pronounced seasonal variation, suggesting that functional genomic traits, rather than taxonomic identity govern species selection. Notably, five MAGs harboured the complete phosphate acetyltransferase-acetate kinase (Pta-Ack) pathway, a critical component of the Wood-Ljungdahl pathway, indicating an underappreciated potential for alternative carbon fixation mechanisms alongside the canonical Calvin-Benson-Bassham cycle. Furthermore, genomic variability, rather than phylogenetic relatedness was the dominant factor shaping cyanobacterial dynamics in the lagoon. This study establishes a direct link between physicochemical fluctuations and cyanobacterial functional diversity, offering critical insights into how climate-driven changes in salinity and nutrient regimes may influence aquatic ecosystems. By elucidating the genomic basis of cyanobacterial adaptation, these findings enhance our capacity to predict ecological outcomes of harmful algal blooms and inform strategies to safeguard ecosystem services in vulnerable coastal habitats. ImportanceThis study employs culture-independent metagenomics to reconstruct cyanobacterial metagenome-assembled genomes (MAGs) in Chilika Lagoon, India, unraveling their spatiotemporal distribution and functional traits. Salinity emerged as the primary driver shaping community structure and functional gene composition, with seasonal fluctuations influencing genes tied to biogeochemical cycling (e.g., carbon, nitrogen) and toxin synthesis. Notably, functional genomic traits--rather than taxonomic identity--governed species selection, highlighting adaptive strategies under environmental stress. Intriguingly, five MAGs harbored the complete Pta-Ack pathway, a component of the Wood-Ljungdahl pathway, suggesting cyanobacteria may employ alternative carbon fixation mechanisms alongside the Calvin-Benson-Bassham cycle under fluctuating conditions. These findings link physicochemical variables (e.g., salinity, nutrients) to functional diversity, revealing how genomic adaptations underpin ecological resilience. The study provides critical insights into cyanobacterial responses to environmental change by bridging microbial genomic plasticity with ecosystem-level impacts. This framework aids in predicting bloom dynamics and toxin risks, offering actionable tools to mitigate ecological threats in vulnerable coastal habitats, thereby informing conservation and management strategies amid climate variability.

microbiology↗

bioRxiv2025

Genomic signatures of terrestrial adaptation in air-breathing catfishes (Clariidae)

Air-breathing catfishes of the family Clariidae exhibit extraordinary adaptations that enable them to survive outside water for extended periods, yet the genetic and genomic basis of these adaptations remain poorly understood. To study these adaptations, we sequenced and assembled two high-quality genomes of two clariid species, Clarias gariepinus and Clarias dussumieri and compare them with previously available genomes of 23 catfish species across nine families. By reconstructing the whole-genome phylogeny and examining patterns of positive selection and gene family evolution, we found unique signatures associated with terrestrial adaptation in clariids. Our analysis revealed that a high proportion of genes were positively selected in clariids, that play critical roles in hypoxia tolerance, thermoregulation, metabolism, and DNA repair, which are key traits for terrestrial adaptation. Additionally, we observed significant expansions in gene families, including Myoglobin (involved in oxygen transport), immunity-related genes, and xenobiotic degradation pathways, highlighting their importance in environmental resilience and detoxification. Together, these findings provide a comprehensive understanding of the genomic changes facilitating the terrestrial adaptation of clariids. This study also highlights the contribution of genome evolution to their resilience, adaptability to novel environments, and invasiveness, offering valuable insights into the genetic basis of ecological niche diversification.

evolutionary biology↗

bioRxiv2023

ALK signalling primes the DNA damage response sensitizing ALK-driven neuroblastoma to ATR inhibition

High-risk neuroblastoma (NB) is a significant clinical challenge. MYCN and ALK, which are often involved in high-risk NB, lead to increased replication stress in cancer cells, suggesting therapeutic strategies. We previously identified an ATR/ALK inhibitor (ATRi/ALKi) combination as such a strategy in two independent genetically modified mouse NB models. Here, we identify an underlying molecular mechanism, in which ALK signalling leads to phosphorylation of ATR and CHK1, supporting an effective DNA damage response. The importance of ALK inhibition is supported by mouse data, in which ATRi monotreatment resulted in a robust initial response, but subsequent relapse, in contrast to a 14-day ALKi/ATRi combination treatment that resulted in a robust and sustained response. Finally, we show that the remarkable response to the 14-day combined ATR/ALK inhibition protocol reflects a robust differentiation response, reprogramming tumour cells to a neuronal/Schwann cell lineage identity. Our results identify a unique ability of ATR inhibition to trigger neuroblastoma differentiation and underscore the importance of further exploring combined ALK/ATR inhibition in NB, particularly in high-risk patient groups with oncogene-induced replication stress.

cancer biology↗

bioRxiv2023

Is It There? - Estimating The Invasion of Armoured Sailfin Catfish (Pterygoplichthys Sp.) in the Water Bodies of Eastern Ghats, India Using eDNA Approach

1.Early detection of invasive species is crucial for effective control of the potential damage they can inflict on the ecosystems. In contrast to the many limitations that traditional detection methods like visual surveys and netting hold, the use of environmental DNA assay provides a powerful alternative. This non-invasive, highly sensitive, and user-friendly technique offers the advantage of detecting invasive species even in areas where direct observation is challenging, thus addressing the shortcomings of traditional techniques and enhancing overall accuracy in estimating distribution. The spread of invasive Pterygoplichthys sp. has become a cause for concern in biodiversity-rich countries like India. Despite this, comprehensive studies on the prevalence of this invasive species are limited. The Eastern Ghats of India remain underexplored with a high potential for supporting diverse lifeforms. Studying the extent of biological invasions in the Eastern Ghats is very essential for effective conservation management to mitigate the ecological and socioeconomic impacts of invasive species. In this study, we have designed and optimised an eDNA-based quantitative PCR assay to map the presence and spread of invasive Pterygoplichthys sp. in selected freshwater ecosystems of the Eastern Ghats. With this assay, we detected invasive Pterygoplichthys sp in almost 65% of the total locations sampled. This study can be further extended to larger geographical areas, which in turn can contribute in formulating necessary measures by the authorities to manage invasion and conserve the diversity of the freshwater ecosystem.

zoology↗

bioRxiv2023

The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neurosecretory protein in the Drosophila CNS.

Numerous roles for the Alk receptor tyrosine kinase have been described in Drosophila, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analysed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk/scRNA-seq and protein datasets from larval brains in which Alk signaling was manipulated, identified a previously uncharacterized Drosophila neuropeptide precursor encoded by CG4577 as an Alk signaling transcriptional target. CG4577, which we named Sparkly (Spar), is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the Drosophila Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (Clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the Drosophila CNS.

developmental biology↗

bioRxiv2023

Genomic potential and evolution of Dissimilatory Nitrate Reduction to Ammonium in Cyanobacteria

Cyanobacteria play an important role in primary production and nitrogen fixation. Although Cyanobacteria are well-known diazotrophic organisms, their role in other steps Nitrogen Cycle is obscure. Screening of Cyanobacterial genomes from cultured and unculturable species can help identify potentially novel functions. In this study, we assembled Cyanobacterial genomes from metagenomic data generated from environmental DNA isolated from a brackish water lagoon (Chilika, India). We annotated these Cyanobacterial metagenome-assembled genomes (MAG) for all the encoded functions using KEGG Orthology. We found two high-quality Cyanobacterial MAGs containing the nirBD gene and nifH and nifD genes involved in the nitrogen cycle. nirBD encodes for the Dissimilatory Nitrate Reduction to Ammonium (DNRA) activity, a function previously not ascribed to Cyanobacteria. We validated the presence of NirBD in publicly available isolate genomes of Cyanobacteria and examined its evolution in the phylum by phylogenetic reconciliation of species and gene trees. Our analysis revealed that both horizontal gene transfers and speciation events contributed to the dispersal of the nirBD gene in Cyanobacteria. We observed that mostly filamentous Cyanobacteria served as ancestral donors in horizontal gene transfer events. Further, we found that the nirBD gene is under a purifying selection pressure in Cyanobacteria. This study demonstrates the genomic potential and evolution of DNRA activity in Cyanobacteria for the utilisation of nitrate in the ecosystem which can help these organisms to cope with extreme environmental conditions. It expands our overall comprehension of the contribution of Cyanobacteria in the biogeochemical cycling in aquatic ecosystems.

microbiology↗

bioRxiv2023

Historical demography and species distribution models shed light on past speciation in primates of northeast India

ObjectivesTo ascertain the effect of historical demography and past climate change as the drivers of diversity in northeast India. Materials and methodsWe took the variant called whole genome files of nine species present in the northeast India from Primate genome sequencing consortium work and assessed each species historic effective population size by using Multiple Sequentially Markovian Coalescent (MSMC) tool. We also constructed species distribution models on past (Pliocene and Pleistocene) and present climate with Maxent, by utilizing publicly available distribution data for each species. ResultsWe got the effective population sizes for 10 million years ago at most, though we considered the data only till 3.3 million years. All species showed rise and decline at various time periods. The species distribution models showed disparate distribution at all three time points with a genera-wise pattern emerging. DiscussionWe found that the evolutionary trajectories of all the four genera into consideration, Macaca, Trachypithecus, Hoolock and Nycticebus are different from each other. Species in Macaca looks to be evolved in northeast as well as come from southeast Asia. Some species of Trachypithecus seems to radiated in the northeast India. Similarly, Hoolock has evolved in the region and Nycticebus is predicted have arrived from Indochina in the region. Hence, this study provides unique insights to the evolutionary dynamics for primate species in the northeast India.

evolutionary biology↗

bioRxiv2021

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

genetics↗

bioRxiv2019

Land Use Change Increases Wildlife Parasite Diversity in Anamalai Hills, Western Ghats, India

Anthropogenic landscape change such as land use change and habitat fragmentation are known to alter wildlife diversity. Since host and parasite diversities are strongly connected, landscape changes are also likely to change wildlife parasite diversity with implication for wildlife health. However, research linking anthropogenic landscape change and wildlife parasite diversity is limited, especially comparing effects of land use change and habitat fragmentation, which often cooccur but may affect parasite diversity substantially differently. Here, we assessed how anthropogenic land use change (presence of plantation, livestock foraging and human settlement) and habitat fragmentation may change the gastrointestinal parasite diversity of wild mammalian host species (n=23) in Anamalai hills, India. We found that presence of plantations, and potentially livestock, significantly increased parasite diversity due possibly to spillover of parasites from livestock to wildlife. However, effect of habitat fragmentation on parasite diversity was not significant. Together, our results showed how human activities may increase wildlife parasite diversity within human-dominated landscape and highlighted the complex pattern of parasite diversity distribution as a result of cooccurrence of multiple anthropogenic landscape changes.

ecology↗