Biology subjects

Soman, A. S.

Publications and source records attributed to Soman, A. S..

3 recordsLinked to original sources

bioRxiv2026

The Landscape of Stop Codon-Free Regions in Primates: A Reservoir of Proto-Genes

Gene duplication has long been viewed as the primary source of new genes, yet growing evidence suggests that de novo emergence from non-coding DNA may be more common than previously assumed, requiring unbiased genome-wide strategies to identify its structural precursors. New protein-coding genes can arise from non-coding DNA, but the sequence features enabling this transition remain unclear. Here, we systematically identify and characterise stop-codon-free regions (SCFRs) across telomere-to-telomere assemblies of human and six other primates. Short SCFRs are abundant and widely distributed, whereas long SCFRs are rare and increasingly associated with coding overlap, moderate GC enrichment, and structured exon-intron contexts. We define exon shadows as in-frame SCFR extensions beyond annotated exon boundaries that lack stop codons, revealing latent coding-compatible sequence adjacent to established exons. We also detect introns fully spanned by single SCFRs, consistent with exitron-like architectures. Repeat composition, codon usage, and Fourier spectral analyses show that length filtering enriches for gene-like features and identifies a subset of long SCFRs with codon-scale periodicity. Together, these findings provide a framework for identifying extended ORF-like regions that may serve as substrates for de novo gene emergence in primates.

genomics↗

bioRxiv2025

Deciphering APOBEC1 in Avians: Unravelling loss events and functional insights

In vertebrates, cytidine-to-uracil (C-to-U) editing is mediated by the AID/APOBEC family of deaminases, with APOBEC1 (A1) known to catalyse precise RNA editing of apolipoprotein B (apoB) transcripts in mammals. Despite its well-characterised role in mammals, the evolutionary history and functional divergence of A1 across birds remain underexplored. Here, we investigate the evolutionary trajectory of A1 in birds, where both the presence of the gene and apoB RNA editing activity have been questioned. Through a comprehensive in silico analysis of 81 avian genomes, we identify recurrent disruptions and catalytic inactivation of A1 in multiple lineages. Comparative sequence and structural analyses reveal a lack of domains and key residues essential for RNA binding, dimerisation, and cofactor interaction, suggesting a role in DNA editing. Furthermore, genome-wide screening for A1-associated G-to-A mutations in long terminal repeat (LTR) retrotransposons demonstrates that species with higher endogenous retrovirus (ERV) loads retain more DNA editing signatures, consistent with a defensive role of A1 against retroelements. In contrast, species with low ERV content exhibit relaxed selection and frequent A1 pseudogenisation. Together, these findings support the hypothesis that DNA editing represents the ancestral function of A1, with RNA editing in mammals evolving later as an exaptation following the expansion of A3 and changes in retroviral pressures.

evolutionary biology↗

bioRxiv2025

Master of none: GPRC6A gene loss is more widespread than previously known

GPRC6A encodes a class C GPCR that can be activated by multiple ligands and potentially acts as a central regulator of diverse metabolic processes by modulating endocrine pathways. Experimental studies have reported numerous distinct functions for GPRC6A, suggesting it may be a key drug target for several metabolic disorders. Yet, the actual function of GPRC6A has been the focus of considerable debate due to contradictory results and the prevalence of loss-of-function mutations in human populations, leading to the perception of GPRC6A as a "Master of none". Interestingly, a genome-wide screen for gene loss events in vertebrate species identified the disruption of the GPRC6A gene in toothed whales, in contrast to widespread conservation in the closely related Bovidae family. We employ a synteny-informed comparative genomic approach to demonstrate that the loss of the GPRC6A gene among mammalian species is more widespread than previously reported, encompassing the entire Bovidae group within Artiodactyla and other fully aquatic mammals, including those belonging to Sirenia. An in-depth search of the genomes and short and long-read sequencing datasets of monotremes, hystricomorphs, rhinolophoid bats, pika, koala, and two shrews (white-toothed pygmy shrew and Asian house shrew) reveals at least nine independent GPRC6A gene loss events in vertebrates, highlighting its lineage-specific dispensability and raising questions regarding its ubiquitous functionality. The evolutionary loss of GPRC6A likely represents a lineage-specific response to specialised diets and ecological niches, reshaping metabolic regulation and taste perception and illuminating how niche specialisation influences gene retention or loss within the GPCR landscape across species.

evolutionary biology↗