Biology subjects

Vijay, N.

Publications and source records attributed to Vijay, N..

At least 19 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↗

bioRxiv2026

WGT-aware analysis reveals increased complexity in the yohimbane biosynthesis pathway of Rauvolfia tetraphylla

Arising from Stander et al. Communications Biology https://doi.org/10.1038/s42003-023-05574-8 (2023) Rauvolfia tetraphylla (Apocynaceae), distributed across Mexico, Tropical America, and Southeast Asia, is known to produce pharmacologically important monoterpene indole alkaloids such as ajmaline, reserpiline, yohimbine, and heteroyohimbanes1. Elucidating the enzymatic pathways2 underlying their biosynthesis is therefore essential for enhancing our understanding of MIA metabolism and enabling their industrial production. In a recent edition of Communication Biology, Stander et al. [STAN23]3 presented a high-quality assembly for R. tetraphylla and uncovered the yohimbane biosynthesis pathway. Based on their proteomics and transcriptomic analysis, two major findings emerged: (1) a medium chain dehydrogenase/reductase (MDR), yohimbane synthase (YOS), produces four yohimbane diastereomers, and (2) three MDR transcripts (MDRT), MSTRG.5530, MSTRG.5531, and MSTRG.5534, along with geissoschizine synthase (GS, MSTRG.5528), can generate a mixture of yohimbane isomers. However, our reanalysis of the raw sequencing reads incorporating haplotype phasing and expression profiling revealed that most candidate genes exist as three homeologous copies with distinct tissue-specific expression. Furthermore, we demonstrate preferential interactions among specific MDRT and GS homeologs, indicating complex cross-subchromosomal enzymatic organisation overlooked in STAN23. Furthermore, several reported candidate genes are chimeric, indicating that incorrect estimation of whole-genome triplication and lack of haplotype phasing can severely limit robust identification and functional characterisation of the yohimbane biosynthetic pathway.

genomics↗

bioRxiv2026

A Benchmarking Framework for Comparative Evaluation of Low-Complexity Region Detection Tools in the Human Proteome

Low-complexity regions (LCRs) are compositionally biased segments of proteins that play critical roles in molecular recognition, structural flexibility, and phase separation. Yet, their accurate detection remains challenging due to methodological variability among computational tools. In this study, we conducted a comprehensive benchmarking of eight widely used LCR detection methods (with different parameter settings) across the Homo sapiens proteome. A modular computational framework was developed to systematically compare LCR characteristics, including residue-centric analyses such as length distributions and coverage percentages. Protein-centric analyses consisted of compositional bias, amino acid composition, and Shannon entropy. Consensus analyses revealed that regions detected by multiple tools were typically longer, more repetitive, and compositionally purer, suggesting stronger structural or functional relevance. Jaccard similarity matrices demonstrated distinct clustering patterns among algorithms based on shared detection principles. Additionally, entropy and purity analyses highlighted fundamental differences in sequence complexity captured by each tool. Together, these results provide a unified, reproducible framework for evaluating LCR detection performance and offer practical guidelines for reliably annotating low-complexity regions in proteome-scale studies.

bioinformatics↗

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↗

bioRxiv2025

De novo genome Assembly of Rauvolfia Serpentina and comparative paleodemographic analysis of Apocynaceae plants

Rauvolfia serpentina is a perennial subshrub widely distributed across Asia and the Indian subcontinent. Belonging to the medicinally important Apocynaceae family, it is renowned for its ecological importance and ethnobotanical applications, especially through the biosynthesis of therapeutic indole alkaloids. In this study, we present a de novo genome assembly and annotation for R. serpentina. The assembled genome comprises approximately 184,000 scaffolds with a scaffold N50 of 7.18 Kbp and a high BUSCO completeness score of [~]90% encompassing [~]22,000 annotated genes. We analysed the paleodemographic histories of nine additional Apocynaceae species using Pairwise Sequentially Markovian Coalescent (PSMC) modelling to place these findings in a broader evolutionary context. This comparative analysis revealed a consistent signature of a pronounced bottleneck across the family during the Mid-Pleistocene glaciations, with few notable species showing high adaptive resilience marked by early recovery in effective population size (Ne), while some even showed secondary Ne peaks in the warmer interglacial periods. Although marked by complex and fairly distinct demographic trajectories, most species exhibit stabilised Ne near the onset of the Holocene. The availability of this high-quality draft genome assembly provides an important resource to advance functional, ecological, and comparative genomics in R. serpentina as well as aid heterologous production of pharmaceutically important biomolecules at an industrial scale, thereby alleviating the pressure on wild populations.

evolutionary biology↗

bioRxiv2025

Chromosomal rearrangements and segmental deletions drive gene loss in squamates

BackgroundGenomic rearrangements, including segmental deletions, duplications, translocations, and inversions of DNA segments, can contribute to gene losses, thereby reshaping genome architecture and potentially resulting in functional consequences. In squamates, karyotypic evolution mainly involves chromosome number reduction through fusions and microchromosome to macrochromosome translocations, although fissions have also contributed to diversification in several lineages. Despite these dynamics, the evolutionary processes and underlying genetic mechanisms driving chromosomal rearrangements and associated gene losses in squamates remain poorly understood. ResultsIn this study, we analysed chromosome/scaffold-level assemblies of 261 squamates, corroborated by short-read, long-read, and transcriptomic data. We found multiple lines of evidence for the putative loss of 53 genes in the squamate lineage. Synteny and phylogenetic analysis revealed that, among the 53 unretrieved orthologs, 14 are lost in squamates with no retained paralog, 15 show ortholog loss with retained paralogs, and 24 remain as unretrieved orthologs. Furthermore, we find that many of the genes lost from squamates are organised in syntenic clusters and are involved in essential immune functions--raising important questions about the role of paralogs in compensating for the function of lost genes, strengthening the "less is more" hypothesis in the squamate lineage. ConclusionsTogether, our comparative genomic analyses highlight that the loss of crucial genes in squamate lineages has occurred primarily through inter- and intrachromosomal rearrangements, including segmental deletions. These findings offer insights into the evolutionary loss of genes involved in macrophage differentiation and inform the development of novel pharmaceutical approaches for modulating immune responses.

genomics↗

bioRxiv2025

Chromatin accessibility differences between the hybrids of nasuta-albomicans complex of Drosophila

Understanding how chromosomal rearrangements (CRs) interact with epigenetic changes to drive speciation is a fundamental question in evolutionary biology. CRs are key contributors to chromosome evolution and can play a pivotal role in reproductive isolation. The Drosophila nasuta-albomicans species complex presents an ideal model to explore this, as D. albomicans possesses neo-sex chromosomes formed by Robertsonian fusion of chr3L, chr3R, and a sex chromosome, unlike its sister species D. nasuta. In this study, we investigate CRs influence on accessible chromatin (AC) and its relationship with genetic differentiation. We used ATAC-seq to decipher ACs of testis in two hybrids of D. albomicans and D. nasuta, and genome-wide fixation index (FST) scans of D. albomicans and D. nasuta to identify regions of genetic differentiation. Our analyses revealed that chromosome 4 (Muller F) harbors the largest number of differentially accessible regions ([~]97 Kb), which coincide with peaks in FST. Moreover, changes in ACs were associated with differential transcription factor (TF) binding across the genome. These results suggest that CRs can drive epigenomic divergence in hybrids, particularly on Muller F, and chromatin-level changes may play a key role in reproductive isolation. Our study provides an example of how chromosomal and epigenetic architecture interact in the early stages of speciation.

evolutionary biology↗

bioRxiv2025

Asian pika populations track local glaciation events through the Pleistocene

BackgroundThe Pleistocene glaciation cycles (2.6 mya - 11 kya) were major climatic events that shaped diversity and community assemblages on Earth. Cold-adapted, high-elevation specialists are expected to have responded negatively to warm interglacial periods, with populations contracting and being pushed up the elevational gradient, leading to isolated populations on mountain tops. During the cool glacial maximums, they are expected to have been distributed at both low and high elevations, with populations expanding and facilitating gene flow across mountains. Pikas (Ochotonidae) are poorly studied high-elevation specialist Lagomorphs being extirpated at alarming rates due to climate change. Insights into their historical demography and current effective population size are crucial in determining their current population status to inform conservation planning. ResultsWe use de novo assembly to construct partial genomes of three Asian pika species (Ochotona ladacensis, O. nubrica, and O. macrotis) that differ in their life history, lifestyle, and social behaviors. We use a combination of species distribution modeling (SDM) projected back in time, in addition to inferring historical demographic patterns using a pairwise sequentially Markovian coalescent (PSMC) approach. Our SDMs predicted the largest bio-climatic niches for all three species during the last glacial maximum (LGM [~]20 kya), and the smallest niches at the last interglacial (LIG[~]120 kya), agreeing well with the elevational shift hypothesis. Our PSMC models for the populations in the Changthang Biotic province (CBP), revealed largely synchronous oscillations of populations sampled in geological timescales but displayed contrasting temporal patterns of population spikes when compared with SDMs. The largest effective population sizes of all species examined on the CBP were inferred to pre-date both the LGM and LIG and were placed around the MIS-6 ([~] 191 kya). After the MIS-6 local glaciation event, populations were inferred to have been through a deep bottleneck, correlating well with local glaciation patterns on this plateau. ConclusionOur study illustrates the power of using complementary approaches to infer historical demography in mountainous landscapes with complex glaciation histories. While SDMs appropriately describe species responses to historical climate across the geographic range of species, PSMCs are more informative about local population dynamics when subject to large degrees of population differentiation. All three species of pikas responded similarly to historical glaciation events on the CBP that differ from the rest of the world and other parts of the Himalayas and likely have very low effective population sizes at current timescales. This is one of the first few studies to examine the population demography of small mammals on the Indo-Tibetan Plateau and has the potential to inform species and population-specific conservation planning in the Himalayas. It is very likely that small mammals such as pikas, marmots and voles on the CBP have low effective population sizes due to historical inbreeding during the LIG and the lack of a glaciation rescue during the LGM. This highlights the need for conservation measures for small mammals on the landscape.

genomics↗

bioRxiv2025

Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss

Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon[boxh]thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of a chromosomal-level genome of the extinct thylacine offers a unique opportunity for such comparative studies. Here, we leverage palaeogenomic data to compare gene presence/absence patterns between the Tasmanian devil and thylacine. We discovered ancestral (between 13-1 Ma) loss of SAMD9L, HSD17B13, CUZD1 and VWA7 due to multiple gene-inactivating mutations, corroborated by short-read sequencing. The loss of SAMD9 correlates with a carnivorous diet, with ancestral gene loss timing mirroring the thylacines shift to hypercarnivory. Our genome-wide analysis reveals olfactory receptor loss and relaxed selection, aligning with reduced olfactory lobes in the thylacine, indicating olfaction is not its primary hunting sense. By integrating palaeogenomic data with comparative genomics, our study reveals ancestral gene losses and their impact on species fitness while providing a foundation for selecting candidate species and genes for thylacine de-extinction. Our approach can be extended to other extinct/endangered species, highlighting genetic factors for de-extinction/conservation efforts.

genomics↗

bioRxiv2024

Evolutionary diversity of CXCL16-CXCR6: Convergent Substitutions and Recurrent Gene Loss in Sauropsids

The CXCL16-CXCR6 axis is crucial for regulating the persistence of CD8 tissue-resident memory T-cells (TRM). CXCR6 deficiency lowers TRM cell numbers in the lungs and depletes ILC3s in the lamina propria, impairing mucosal defence. This axis is linked to diseases like HIV/SIV, cancer, and COVID-19. Together, these highlight that the CXCL16-CXCR6 axis is pivotal in host immunity. Previous studies of the CXCL16-CXCR6 axis found genetic variation among species but were limited to primates and rodents. To understand the evolution and diversity of CXCL16-CXCR6 across vertebrates, we compared [~]400 1-to-1 CXCR6 orthologs spanning diverse vertebrates. The unique DRF motif of CXCR6 facilitates leukocyte adhesion by interacting with cell surface-expressed CXCL16 and plays a key role in G-protein selectivity during receptor signalling; however, our findings show that this motif is not universal. The DRF motif is restricted to mammals, turtles, and frogs, while the DRY motif, typical in other CKRs, is found in snakes and lizards. Most birds exhibit the DRL motif. These substitutions at the DRF motif affect the receptor[boxh]Gi/o protein interaction. We establish recurrent CXCR6 gene loss in 10 out of 36 bird orders, including Galliformes and Passeriformes, Crocodilia, and Elapidae, attributed to segmental deletions and/or frame-disrupting changes. Notably, single-cell RNA sequencing of the lung shows a drop in TRM cells in species with CXCR6 loss, suggesting a possible link. The concurrent loss of ITGAE, CXCL16 and CXCR6 in chickens may have altered CD8 TRM cell abundance, with implications for immunity against viral diseases and vaccines inducing CD8 TRM cells.

immunology↗

bioRxiv2024

A preliminary assessment of the genome sequence of the Annual Mercury, Mercurialis annua

SummaryReview of Christenhusz et al., Wellcome Open Research. A high-quality genome sequence of the Annual Mercury, Mercurialis annua is generated as part of the Darwin Tree of Life Project. The Annual Mercury plant is a good study system for evolutionary transitions between sexual systems, mechanisms of sex determination in plants and changes in ploidy level. The XX female sequenced in this study provides a chromosome-level assembly with reasonable contiguity and high gene completeness. We compare the gene completeness of the assembly presented with those of closely related species, including another published assembly of the Annual Mercury generated using a polyploid individual. Annotation and comparative analysis of the organelle genomes suggest complete circular assemblies. However, we note that the NCBI submissions are tagged as linear. The repeat content identified on the autosomes and X chromosome appears comparable, suggesting the sex chromosomes are relatively recent. An alternative possibility is that our preliminary analysis failed to identify repeats unique to the X chromosome or that these repeat regions have not been assembled in the genome. The harder-to-assemble centromere and telomere regions are not annotated in the genome and are potentially incomplete or missing. We identify putative centromere regions with elevated GC content, but they must be validated. The demographic histories reconstructed for the autosomes and X suggest distinct trajectories irrespective of the scaling parameters. Compared to the autosomes, the older histories recorded on the X are a promising avenue for further work to study the origin of the sex chromosome. Our preliminary assessment of the genome sequence suggests the genome is of sufficiently good quality for use as a reference for diverse analysis aimed at answering important eco-evolutionary questions of interest that can be answered using this system.

genomics↗

bioRxiv2024

What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken?

ARISING FROM Zhu, F., Yin, ZT., Zhao, QS. et al. Communications Biology https://doi.org/10.1038/s42003-023-05619-y (2023) High-quality chromosome-level genome assemblies for numerous avian species promise to address longstanding questions in bird evolution and biology. In a recent issue of Communications Biology, Zhu, F., Yin, ZT., Zhao, QS. et al. (ZYZSJ)1 presented a chromosome-level assembly for the Silkie chicken using a multi-platform high-coverage dataset to obtain accurate and complete sequences spanning the entire genome. A key finding from their genomic analysis is the reconstruction of the structure of the complex rearrangement at the Fm locus, the primary genetic change underlying the rare and conspicuous dermal hyperpigmentation phenotype generally called Fibromelanosis. However, in contrast to their identification of the *Fm_1 scenario, several previously published studies2-6 claim that *Fm_2 is the valid scenario. Our re-analysis of ZYZSJs new assembly (CAU_Silkie) using long-read data from multiple black-bone chickens demonstrates that *Fm_2 is the correct scenario. The *Fm_1 scenario favoured by ZYZSJ results from an assembly error caused by mosaic haplotypes generated during the de novo assembly step. We recommend post-assembly validation and correction in genome projects to prevent misinterpretation due to assembly artefacts. Enhancing the assembly of haplotypes in such complex regions is essential for unravelling the genetic foundations of traits governed by genes within these areas.

genomics↗

bioRxiv2023

Common Ancestry of the Id Locus: Genetic Clues and Polygenic Possibilities

The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a [~]1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.

genomics↗

bioRxiv2023

Patterns of low-complexity regions in human genes

Genome evolution stands as a paramount determinant for species survival and overall biodiversity on Earth. Among the myriad processes orchestrating genome evolution, the dynamic attributes of length and compositional polymorphism within low-complexity regions (LCR) are the fastest. Clusters of LCR hotspots serve as pivotal conduits connecting different modes of genome evolution, specifically arising through gene duplication events and harboring pivotal sites susceptible to point mutations. Thus, they offer a holistic perspective on the panorama of genome evolution. Furthermore, LCR actively participates in a multifaceted spectrum of neurological, developmental, and cognitive disorders. Despite the substantial body of knowledge concerning the roles of individual LCR-containing genes in the causation of diseases, a comprehensive framework remains conspicuously absent, failing to provide a unified portrayal of LCR-containing genes and their interactions. Furthermore, our understanding of the intricate interplay between paralogy and LCR remains notably deficient. Within this study, we have identified nine clusters of LCR hotspots within the human genome. These clusters are predominantly comprised of closely positioned paralogs, characterized by a significantly higher prevalence of shared LCR and a lower degree of differentiation (FST) across diverse human populations. Moreover, we have unveiled intricate networks of LCR-containing genes engaged in mutual interactions, sharing associations with a spectrum of diseases and disorders, with a particular emphasis on hereditary cancer-predisposing syndromes. Our discoveries shed light on the compelling potential of LCR-containing interacting genes to collectively engender identical diseases or disorders, thereby underscoring their pivotal role in the manifestation of pathological conditions. Significance StatementAmong myriad genome evolution processes, low-complexity regions (LCR) are pivotal, being both the fastest and bridging other evolution modes like gene duplication and point mutations. Understanding LCR-containing paralogous genes is essential to comprehend genetic diseases. Here, we demonstrate that the human genome harbors clusters of LCR hotspots mainly composed of paralogous genes sharing LCR, indicating a role for segmental duplication. The degree of differentiation is significantly lower in clusters of LCR hotspots than in other regions. Moreover, we provide a detailed network of LCR-containing interacting genes associated with shared diseases. Instead of attributing a single disease to an LCR gene, a unified perspective on LCR-containing interacting genes causing the same disease enhances our understanding of LCR-induced disease mechanisms.

evolutionary biology↗

bioRxiv2023

Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766)

The green peafowl (Pavo muticus, Linnaeus 1766) is an endangered species native to the forests of tropical Southeast Asia. Although its morphological diversity and subspecies categorization is known and built upon traditional taxonomy, the intraspecific genetic structure has not been comprehensively addressed. To assess if phenotypic diversity is reflected at the molecular level, we used public whole-genome sequencing data of one blue peafowl and 52 green peafowls from multiple countries to characterize their genetic diversity, differentiation, identify Ancestry Informative Markers (AIMs) and compare their demographic histories. We found evidence of substantial population structure, with at least three distinct clusters and diverse demographic histories that may mirror different responses to various biogeoclimatic events. The genetic structure of native populations follows the pattern of the geographic distribution of the green peafowl with the highest autosomal pairwise FST between Yunnan and Vietnam ([~]0.1) and intermediate estimates for Thailand comparisons ([~]0.077). We identify AIMs to distinguish between these three native populations. The captive green peafowls from Xinxing clustered with Vietnam and those from Qinhuangdao (QHD) formed a separate cluster. The two QHD individuals appear to have varying levels of blue peafowl ancestry based on PCA and admixture analysis and are mirrored in their demographic histories. Our study establishes the occurrence of genetically distinct natural populations of green peafowl that can be considered separate management units (MU) when planning conservation actions. Transboundary cooperation and concerted efforts to foster genetic diversity are imperative for Southeast Asian species at risk.

genomics↗

bioRxiv2023

Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl

Small and midsize deletions and insertions (InDels) are major events that play a crucial role in the evolution of genome size and contribute to the genetic and phenotypic diversity of species. In recent years, considerable attention has been given to studying small indels associated with various developmental, growth, and production traits in domestic chicken breeds. Additionally, small and midsize indels have been studied between chicken and phylogenetically more distant species such as duck, turkey, rock pigeon, and other passerine birds. However, the investigation of small and midsize deletions in the wild relatives of chickens has been relatively overlooked until now. To address this gap, our study aimed to identify the presence and distribution of midsize deletions (> 1 Kb) in the wild relatives of chickens. We conducted a comparative genomic analysis using high-quality genomic data from four species belonging to the Gallus genus. Our analysis revealed the existence of more than 125 midsize deletions in the three other species compared to Gallus gallus (red junglefowl). These midsize deletions were found to be distributed in intergenic regions and within introns of various protein-coding genes but not in the exonic regions of protein-coding genes. Furthermore, we observed a trend between the number of midsize deletions and the phylogenetic distance in the phylogeny of the Gallus genus. The most ancestral species, Gallus varius (green junglefowl), exhibited the highest deletions, followed by Gallus lafayettii (Ceylon junglefowl) and Gallus sonneratii (grey junglefowl). Some protein-coding genes harboring deletions in their introns and upstream regions were associated with body development, production, growth traits, abdominal fat deposition, behavioral patterns such as stress, fear, anxiety, plumage color, and adaptation to extreme climatic conditions. Our study finds that the midsize deletions identified in wild relatives of red junglefowl contribute less than 1% of DNA loss with a rate of 8-44 Kb/My during the evolution of the Gallus genus.

genomics↗

bioRxiv2023

Terminal regions of a protein are a hotspot for low complexity regions (LCRs) and selection

A majority of the protein-coding genes consist of low-complexity regions (LCRs) in eukaryotes. Volatile LCRs are a novel source of adaptive variation, functional diversification, and evolutionary novelty. LCRs contribute to a wide range of neurodegenerative disorders. Conversely, these regions also play a pivotal role in critical cellular functions, such as morphogenesis, signaling, and transcriptional regulation. An interplay of selection and mutation governs the composition and length of LCRs. High %GC and mutations provide length variability because of mechanisms like replication slippage. The selection is nearly neutral for expansion/contraction within the normal range and purifying above a critical length. Because of the complex dynamics between selection and mutation, we need a better understanding of the coexistence and mechanisms of the two. Our findings indicate that site-specific positive selection and LCRs prefer the terminal regions of a gene and co-occur in most of the Tetrapoda clades. Interestingly, positively selected sites (PSS) are significantly favored in LCRs in eight of the twelve clades studied. We also observed a significant favor of PSSs in the polyQ region of MAML2 in five clades. We also found that PSSs in a gene have position-specific roles. Terminal-PSS genes are enriched for adenyl nucleotide binding, while central-PSS genes are involved in glycosaminoglycan binding. Moreover, central-PSS genes mainly participate in defense responses, but terminal-PSS genes are non-specific. LCR-containing genes have a significantly higher %GC and lower {omega} (dN/dS) than genes without repeats across the Tetrapoda clade. A lower {omega} suggests that even though LCRs provide rapid functional diversity, LCR-containing genes face intense purifying selection.

genomics↗