Biology subjects

Dhakad, P.

Publications and source records attributed to Dhakad, P..

4 recordsLinked to original sources

bioRxiv2026

Horizontal transfer of an antimicrobial peptide across insects

Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.

evolutionary biology↗

bioRxiv2025

Predictors of protein evolution in the drosophilid immune system

The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understood. Here, we applied a meta-analytic mixed model approach to quantify how immune-pathway genes differ from other genes in their rates of protein sequence divergence (dN/dS), evidence for positive selection, and gene turnover rate ({lambda}), while simultaneously accounting for gene length, expression level, genetic and protein-protein interactions, and structural features such as relative solvent accessibility (RSA). In general, rates of sequence evolution were strongly and positively associated with RSA, and negatively with gene length, expression, and genetic/protein-protein interactions, while gene turnover rate was largely unaffected by these factors. We find immune genes evolved significantly faster at the protein sequence level than non-immune genes, but contrary to our expectation exhibited lower gene turnover rates. Functional and pathway-level analyses revealed accelerated evolution in effectors, receptors, and antiviral genes, with cGAS-STING and Toll pathways showing the highest dN/dS. Gene turnover rate was elevated only in effectors, whereas cellular defence genes were particularly conserved. We also found evidence for elevated proportion of sites under episodic positive selection in immune genes, particularly in effectors, indicating ongoing adaptive diversification. These findings highlight how immune diversification in Drosophilidae arises from multiple, partly independent evolutionary axes, shaped jointly by structural constraints, functional roles, and lineage-specific pathogen pressures.

molecular biology↗

bioRxiv2025

Transcriptomic analysis of non-model Drosophilidae reveals novel AMP candidates

BackgroundDrosophila melanogaster has been a valuable model for dissecting the molecular architecture of innate immunity. However, the family Drosophilidae encompasses over 4000 species, spanning deep evolutionary divergences and diverse ecologies. Here, we use immune challenge with the gram-negative pathogen Providencia rettgeri to investigate the conservation and evolution of immune responses in three non-model drosophilid species that diverged from D. melanogaster over 45 million years ago--Hirtodrosophila cameraria, H. confusa, and Scaptodrosophila deflexa. ResultsWe find that all three species retain a core set of immune signaling and recognition genes, but exhibit substantial variation in effector gene content and inducibility. In particular, Scaptodrosophila deflexa lacks orthologs of multiple antimicrobial peptides (AMPs) known from D. melanogaster, including DptA, AttA, and AttC, and shows little transcriptional response to bacterial-challenge with Providencia rettgeri. In contrast, both of the Hirtodrosophila species exhibit substantial transcriptional responses, including strong induction of canonical Imd pathway genes. Microbiome profiling of our samples revealed higher Providencia abundance in H. cameraria, and high levels of the defensive symbiont Spiroplasma in S. deflexa--potentially explaining differences in infection outcome. Our combined annotation and expression analysis of these species also allowed us to identify 20 novel AMP-like candidates, many with structural features like known AMPs. ConclusionsOur study demonstrates the feasibility of functional immune analyses in non-model Drosophila species and reveals striking lineage-specific differences in immune gene repertoire and expression. These findings highlight the importance of non-model, wild-derived taxa for uncovering novel immune effectors and understanding evolutionary forces shaping insect immunity.

evolutionary biology↗

bioRxiv2025

Comparative gene annotation of 304 species of Drosophilidae

High-quality genome annotations are essential if we are to address central questions in comparative genomics, such as the origin of new genes, the drivers of genome size variation, and the evolutionary forces shaping gene content and structure. Here, we present protein-coding gene annotations for 301 species of the family Drosophilidae, generated using the Comparative Annotation Toolkit (CAT) and BRAKER3, and incorporating available RNA-seq and protein evidence. We take a comparative phylogenetic approach to annotation, with the aim of improving consistency and accuracy, and to generate a robust set of gene annotations and orthology assignments. We analyze our annotations using a phylogenetic mixed-model approach and find that gene number and CDS length exhibit moderate phylogenetic heritability (40% and 9.7%, respectively). For comparison, we also present analyses using a subset of the 215 highest quality genomes, although the findings were not markedly different. Our work suggests that while evolutionary history contributes to variation in these traits, species-specific factors--including assembly error--play a substantial role in shaping observed differences. To illustrate the utility of our annotations for comparative analyses, we investigate codon usage bias and amino acid composition across Drosophilidae. We find that codon usage is correlated with overall GC content and evolves slowly, but that it is also strongly shaped by selection--such that, in general, species with the strongest selection on synonymous codon usage show the lowest GC bias in third codon positions. This comparative annotation dataset forms part of an on-going collaborative project to sequence and annotate all species of Drosophilidae, with data and annotations being made rapidly and freely available on an on-going basis. We hope that this effort will serve as a foundation for studies in evolutionary and functional genomics and comparative biology across Drosophilidae.

genomics↗