Biology subjects

Giri, G.

Publications and source records attributed to Giri, G..

6 recordsLinked to original sources

bioRxiv2026

Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects

Satellite DNAs (satDNAs) are tandemly repeated sequences that can comprise large fractions of eukaryotic genomes. For decades, we have known that satellite DNAs are among the most rapidly evolving genomic components, yet few studies have examined their dynamics across broad evolutionary frameworks--likely in part because their rapid evolution complicates or precludes homology identification. We investigated satDNA dynamics across 50 ground beetle (Carabidae) species, sampling above and below the species level in the subgenus Plataphus of Bembidion. We used RepeatExplorer2 and a novel homology detection pipeline, which we validated using species of Drosophila for which satDNAs are well-documented, to study satDNA dynamics in a comparative framework. We show that satDNAs comprise large genomic fractions (mean = 25.7%, range = 3.2%-53%), with individual satDNA motifs accounting for >30% of total DNA within some species. We quantify major satDNA turnover among closely related species which drives extensive repatterning of repeat content over short evolutionary scales. To place our findings in a broader context, we also surveyed satDNA diversity across the beetle suborder (Adephaga), the beetle order (Coleoptera), and the next six largest insect orders (Lepidoptera, Diptera, Hymenoptera, Hemiptera, Orthoptera, Trichoptera), representing 400 additional species. While satDNA abundance was significantly elevated in the focal subgenus (Plataphus), high genomic proportions were also found in species across Adephaga, Coleoptera, Hymenoptera, and Diptera. Conversely, satDNA proportions were notably reduced in Lepidoptera and Trichoptera. Our investigation of satDNA dynamics at narrow and broad taxonomic scales provides a quantitative illustration of satDNA turnover across a well-sampled clade. It also identifies new high-potential systems for gaining mechanistic insights into the drivers and impacts of satDNA evolution, and raises questions regarding potential links between satDNA turnover, speciation, and core strategies of chromosome and genome architecture in diverse clades.

evolutionary biology↗

bioRxiv2025

Conserved molecular signatures of hygrosensory neurons in two dipteran species

Small poikilothermic animals like insects rely on environmental sensing for survival. The ability to detect humidity and temperature through specialized sensory neurons is particularly critical, allowing them to maintain water balance across diverse environments. While recent studies have identified key receptors associated with humidity sensing, our understanding of the broader molecular architecture underlying these sensory systems remains incomplete. Here, we conducted a comparative analysis of humidity receptor neurons (HRN) between the vinegar fly Drosophila melanogaster and the yellow fever mosquito Aedes aegypti. We identified 21 genes that define the molecular identity of HRNs. These genes encode proteins involved in transcriptional regulation, cellular signaling, enzymatic pathways and cellular organization. Through behavioral analysis, we demonstrate essential roles for three of these genes, the serotonin receptor 5-HT7, the transcription factor nubbin and the kinesin motor protein Kif19A are all required for humidity-guided behavior. The conservation of this molecular toolkit between species separated by over 200 million years of evolution suggests shared functional requirements for environmental sensing in insects. Our findings provide insights into fundamental principles of sensory neuron organization and oeer a framework for understanding how specialized sensory systems evolve and maintain their function.

animal behavior and cognition↗

bioRxiv2024

Humidity-dependent structural adaptations of Drosophila melanogaster hygrosensilla

Understanding how organisms detect environmental humidity remains a fundamental problem in sensory biology. While specialized sensory neurons in insect antennae can detect changes in humidity, the mechanism underlying this ability is not fully understood. Here, we present an integrated approach combining precise humidity control, rapid cryo-preservation, and serial block-face scanning electron microscopy (SBF-SEM) to investigate the ultrastructure of hygrosensilla in the vinegar fly Drosophila melanogaster. We developed a deep learning-based segmentation pipeline to analyze three-dimensional structural features of sensilla exposed to different humidity conditions at stable temperature. Our analysis reveals consistent differences in sensilla width between high (80% RH) and low (26% RH) humidity conditions across all chambers of the sacculus. Additionally, we identified chamber-specific patterns in sensilla tapering, indicating specialized structural adaptations across different sensilla populations. The observed structural changes suggest a potential role for mechanical transduction in humidity sensing. This study establishes a technical framework for high-resolution analysis of sensory organs while providing new insights into the structural basis of humidity detection. Our findings advance our understanding of how specialized sensory organs might transduce environmental signals into neural responses.

neuroscience↗

bioRxiv2024

Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro

While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.

evolutionary biology↗

bioRxiv2023

A dynamic humidity arena to explore humidity related behaviours in insects

Humidity is a critical environmental factor influencing the behaviour of terrestrial organisms. Despite its significance, the neural mechanisms and behavioural algorithms governing humidity sensation in insects remain elusive. In this study, we introduce a novel dynamic humidity arena to investigate humidity-guided behaviour in the vinegar fly Drosophila melanogaster. The arena allows precise humidity control, low error rates, and fast settling times, making it a robust tool for studying humidity-related behaviours. Our results reveal that desiccated and starved flies (DS flies) search for higher relative humidity environments (65-75%) while sated flies tend to stay within their initial environments. In contrast, Ionotropic receptor (Ir)93a mutant flies with impaired humidity sensing show no preference to relative humidity. The search for higher humidity in DS flies is reflected in their relatively high displacement and walking speed compared to control and mutant flies. Our novel method manipulates humidity cues to create complex humidity landscapes that respond in real-time to insect movement. This will help us shed light on how humidity shapes behaviour and offers a foundation for further research in the field of hygrosensation.

neuroscience↗

bioRxiv2023

Adaptive genomic variation is linked to a climatic gradient in a social wasp

Species vary in their ability to adapt to rapid changes, with the presence of genetic variation often facilitating long-term evolutionary responses. Given the impending threat of climate change, it is critical to investigate how genetic variation facilitates persistence and possible range expansion in animals. Here, we combine genomic and climatic data to characterize the drivers of local adaptation in the widely distributed, social wasp Mischocyttarus mexicanus cubicola. Using whole genome sequence data, we show that adaptive genomic variation is linked to a climatic gradient across the broad distribution of this species. We found strong population structure, dividing the species into two genetic clusters that follow subtropical and temperate regions. Patterns of gene flow across the range deviate from those expected by isolation by distance alone with climatic differences resulting in reduced gene flow even between adjacent populations. Importantly, genotype-environment analyses reveal candidate single nucleotide polymorphism (SNPs) associated with temperature and rainfall, suggesting adaptation for thermal and desiccation tolerance. In particular, candidate SNPs in or near mitochondrial genes ND5, CO1, and COIII are linked to cold tolerance and metabolism. Similarly, the Gld nuclear gene shown to mediate cold hardiness and cuticle formation, shows two candidate SNPs with non-synonymous mutations unique to temperate populations. Together, our results reveal candidate SNPs consistent with local adaptation to distinct climatic conditions. Thus, the integration of genomic and climatic data can be a powerful approach to predict vulnerability and persistence of species under rapid climate change.

evolutionary biology↗