Biology subjects

Patil, A. B.

Publications and source records attributed to Patil, A. B..

7 recordsLinked to original sources

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

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↗

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↗

bioRxiv2022

Jack of all trades: genome assembly of Wild Jack and comparative genomics of Artocarpus

Known as breadfruits for their diverse nutritious fruits, the Artocarpus (Moraceae) genus is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a large tree, Artocarpus hirsutus, also called "Wild jack" or "Ayani" is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from sacred groves of Coorg, India. We compared our Wild jack genome with previously published Jackfruit and Breadfruit genomes to decipher demography and evolution. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which results in its larger genome size. Gene family evolution and signatures of selection identified multiple genes from starch, sucrose metabolism, plant hormone signal transduction, etc., in Artocarpus species. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild jack.

genomics↗

bioRxiv2022

Genome divergence across the Indo-Burman arc: a tale of two peacocks

Exaggerated traits of the peacock are attributed to sexual selection. Yet, the two species of Asian peacock are conspicuously different in their plumage colouration and level of sexual dichromatism. Our integrative comparative study of bird calls, morphological differences and genomic divergence between the Indian blue peafowl and the green peafowl suggests a strong role of habitat differences in shaping species-specific changes. We estimate a recent (1-3 MYA) split of these species in the Pliocene or early Pleistocene, followed by intermittent periods of gene flow. Despite the relatively recent split, the high levels of genomic differentiation (FST [~] 0.6) mirror the divergence in morphological traits. Several genes involved in body patterning and colouration have accumulated protein-coding differences between the peacock species. Our estimates suggest genetic diversity in the widespread Indian peafowl ({theta}w [~] 0.0015) is comparable but slightly higher than in the endangered green peafowl ({theta}w [~] 0.0012). The ratio of genetic diversity on the Z chromosome to the autosomes (Z/A) is consistent with a polygynous mating system in the Indian peafowl compared to monogamy in the green peafowl. The Asian peacock species continue to provide exciting new insights into speciation and mating system evolution in the post-genomic era.

evolutionary biology↗

bioRxiv2022

Birth and Death in Terminal Complement Pathway

The cytolytic activity of the membrane attack complex (MAC) has a crucial role in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrate C6 gene. The subsequent duplication and divergence of this vertebrate C6 gene formed the C7, C8, C8{beta}, and C9 genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered that C9 has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at the C9 locus. In this study, we have generated a >120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of the C9 gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons of C9 in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred after C9 gene loss in an early galliform ancestor. Our study of C6 gene birth in an early vertebrate ancestor and C9 gene death in galliform birds provides insights into the evolution of the TCP.

immunology↗

bioRxiv2020

CoalQC - Quality control while inferring demographic histories from genomic data: Application to forest tree genomes

Estimating demographic histories using genomic datasets has proven to be useful in addressing diverse evolutionary questions. Despite improvements in inference methods and availability of large genomic datasets, quality control steps to be performed prior to the use of sequentially Markovian coalescent (SMC) based methods remains understudied. While various filtering and masking steps have been used by previous studies, the rationale for such filtering and its consequences have not been assessed systematically. In this study, we have developed a reusable pipeline called "CoalQC", to investigate potential sources of bias (such as repeat regions, heterogeneous coverage, and callability). First, we demonstrate that genome assembly quality can affect the estimation of demographic history using the genomes of several species. We then use the CoalQC pipeline to evaluate how different repeat classes affect the inference of demographic history in the plant species Populus trichocarpa. Next, we assemble a draft genome by generating whole-genome sequencing data for Mesua ferrea (sampled from Western Ghats, India), a multipurpose forest plant distributed across tropical south-east Asia and use it as an example to evaluate several technical (sequencing technology, PSMC parameter settings) and biological aspects that need to be considered while comparing demographic histories. Finally, we collate the genomic datasets of 14 additional forest tree species to compare the temporal dynamics of Ne and find evidence of a strong bottleneck in all tropical forest plants during Mid-Pleistocene glaciations. Our findings suggest that quality control prior to the use of SMC based methods is important and needs to be standardised.

evolutionary biology↗