Arising from Stander et al. Communications Biology https://doi.org/10.1038/s42003-023-05574-8 (2023) Rauvolfia tetraphylla belongs to the Apocynaceae family, one of the largest plant families distributed across Mexico, Tropical America and Southeast Asia. They are known for producing pharmacologically important monoterpene indole alkaloids (MIAs), such as ajmaline, reserpiline, yohimbine and heteroyohimbanes 1 . Due to their pharmaceutical properties, the biosynthetic modalities of several of these secondary metabolites have been explored 2 , however, the enzymatic pathways underlying yohimbine production have remained fairly understudied. Elucidating these pathways is therefore critical to enhance our understanding of yohimbane MIA metabolism and aid in their industrial production and drug discovery. This research gap was adequately addressed in a recent edition of Communication Biology , where Stander et al. [STAN23] 3 presented a high-quality assembly for R. tetraphylla using a multi-platform high-coverage dataset. Notably, the yohimbane biosynthesis pathway was uncovered for the first time. Based on their metabolomics, proteomics and transcriptomic analysis followed by in vitro biochemical assays, two major findings emerged: (1) A medium chain dehydrogenase/reductase (MDR), yohimbane synthase (YOS) was found that produces a mixture of four diastereomers of yohimbanes (2) Three MDR transcripts (MDRT), MSTRG.5530, MSTRG.5531, and MSTRG.5534 were identified, which, in conjunction with geissoschizine synthase (GS, MSTRG.5528), produce a mixture of yohimbane isomers. However, the well-foundedness of the results is limited by a methodological oversight: the study does not take into account an independent whole-genome triplication event (WGT) in R. tetraphylla other than the one shared across Eudicotyledons, thus limiting the candidates identified in yohimbane biosynthesis and undermining the complexity of the biosynthetic modalities 4,5 .

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.

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 (under multiple 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 distribution and coverage percentage. Protein-centric analyses included 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 revealed 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 reliable annotation of low-complexity regions in proteome-scale studies.

Distal renal tubular acidosis (dRTA) is a heterogeneous group of disorders of impaired distal acid secretion, leading to normal anion gap metabolic acidosis, growth failure and nephrocalcinosis. Although a genetic basis is well established, the genetic aetiology may differ in Asian populations; however, large multicenter studies from Asia are limited. This multicenter observational study, conducted under Indian Council of Medical Research Task Force on Rare Diseases, included incident and prevalent cases of dRTA between 2020 and 2024. Detailed clinical, biochemical, genetic, and outcome data were analysed. Of 96 children initially suspected to have dRTA, five were reclassified following next-generation sequencing. The remaining 91 cases were diagnosed as dRTA. Genetic testing identified pathogenic/likely pathogenic variants in 56 (61.5

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.

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.

Background Genomic 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. Results In this study, we analysed chromosome/scaffold-level assemblies of 265 squamates, corroborated by short-read, long-read, and transcriptomic data. We found multiple lines of evidence for the absence of 53 genes in the squamate lineage. Notably, increased genomic rearrangement activity appears to be associated with the squamate-specific loss of these genes, including IL34 , STAP1 , LAPTM5 , and TNIP2, which are key regulators of macrophage activation and polarisation. Most of the missing genes were intact in tuatara and other vertebrate species. Furthermore, we find that many of the genes missing from squamates are organised in syntenic clusters and are involved in essential immune functions—raising important questions about whether their absence in squamates reflects true gene loss or simply results from incomplete assemblies. Conclusions Together, 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. ### Competing Interest Statement The authors have declared no competing interest. * EBR : Evolutionary Breakpoint Region HBV : Hepatitis B Virus MYA : Million Years Ago TCR : T Cell Receptor PacBio : Pacific Biosciences ONT : Oxford Nanopore Technologies FDR : False Discovery Rate BH : Benjamini–Hochberg correction NCBI : National Center for Biotechnology Information BLASTn : Basic Local Alignment Search Tool (nucleotide) MAF : Multiple Alignment Format IGV : Integrative Genomics Viewer RNA-seq : RNA sequencing Mb : Megabase Kb : Kilobase Department of Biotechnology, Ministry of Science and Technology, India, BT/11/IYBA/2018/03 Science and Engineering Research Board, ECR/2017/001430

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.

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. ### Competing Interest Statement The authors have declared no competing interest. Department of Biotechnology, https://ror.org/03tjsyq23, BT/11/IYBA/2018/03 Science and Engineering Research Board, https://ror.org/03ffdsr55, ECR/2017/001430

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-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 timing of gene loss mirrors the thylacine's shift towards hypercarnivory and increased body size. Notably, the loss of SAMD9 correlates with a carnivorous diet. 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 survival and resilience to environmental changes. Our approach can be extended to other extinct and endangered species, helping to identify genetic factors for conservation efforts.

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. ### Competing Interest Statement The authors have declared no competing interest. WOS-A Project - Life Sciences, Department of Science and Technology, SR/WOS-A/LS-225/2018(G)

Volatile low complexity regions (LCRs) are a novel source of adaptive variation, functional diversification and evolutionary novelty. An interplay of selection and mutation governs the composition and length of low complexity regions. High %GC and mutations provide length variability because of mechanisms like replication slippage. Owing to the complex dynamics between selection and mutation, we need a better understanding of their coexistence. Our findings underscore that positively selected sites (PSS) and low complexity regions prefer the terminal regions of genes, co-occurring in most Tetrapoda clades. We observed that positively selected sites within a gene have position-specific roles. Central-positively selected site genes primarily participate in defence responses, whereas terminal-positively selected site genes exhibit non-specific functions. Low complexity region-containing genes in the Tetrapoda clade exhibit a significantly higher %GC and lower ω (dN/dS: non-synonymous substitution rate/synonymous substitution rate) compared with genes without low complexity regions. This lower ω implies that despite providing rapid functional diversity, low complexity region-containing genes are subjected to intense purifying selection. Furthermore, we observe that low complexity regions consistently display ubiquitous prevalence at lower purity levels, but exhibit a preference for specific positions within a gene as the purity of the low complexity region stretch increases, implying a composition-dependent evolutionary role. Our findings collectively contribute to the understanding of how genetic diversity and adaptation are shaped by the interplay of selection and low complexity regions in the Tetrapoda clade.

Summary Review 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. ### Competing Interest Statement The authors have declared no competing interest.

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 approximately 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—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.

The availability of high-quality chromosome-level genome assemblies of an increasing number of avian species holds significant promise for addressing longstanding questions in bird evolution and biology. In a recent issue of Communications Biology , Zhu, F., Yin, ZT., Zhao, QS. et al. (ZYZSJ)[1][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 chicken 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 (which the authors refer to as FM2) as the correct arrangement at the Fm locus, several previously published studies[2][2]–[6][3] claim that * Fm\_2 is the valid scenario. Our re-analysis of ZYZSJ’s new genome assembly (CAU\_Silkie) demonstrates that * Fm_2 is indeed the correct scenario, and 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 that genome projects perform post-assembly validation and correction to safeguard biological interpretations from the impact of assembly artefacts. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-6