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At least 19 recordsLinked to original sources
PubMed2025

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-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.

Animals↗
PubMed2026

Genomic contingence beneath ecological convergence: the tempo and mode of gene loss in parasitic bilaterians.

Parasitism has independently evolved hundreds of times among metazoans. Nonetheless, parasites have explored only a limited range of ecologies, and they display frequent convergence in morphological, behavioral, and life-history traits. Although gene loss in particular parasitic species has been documented, it is not known if gene loss converges along the same lines as these other traits. To test for convergent gene loss, we characterized the housekeeping, regulatory, and DNA-repair complements of 48 bilaterian species, including 20 parasites belonging to 6 different bilaterian phyla. We found that different parasitic strategies do not display characteristic tempos or modes of gene loss. Further, the accelerated rates of gene loss seen in some parasites were almost always shared with their free-living relatives, indicating that the increased rate of loss preceded the rise of parasitism. Therefore, the convergent ecological strategies and adaptations that have arisen in distantly related parasitic lineages overlay contingent gene losses, which largely reflect their phylogenetic history. These results have important implications for how ecologists and evolutionary biologists should model the acquisition of parasitism, especially regarding the long-held assumption that reversion from a parasitic to a free-living state is impossible.

Animals↗
PubMed2026

Sequential gene loss promotes expansion of monophasic Salmonella Typhimurium ST34.

Understanding the genetic factors facilitating emergence of infectious diseases is critical, however, mechanisms underlying expansion of pathogenic bacterial variants remain unclear. Here we performed a large-scale genomic analysis of 44,597 Salmonella Typhimurium genomes and observe that sequential gene loss in monophasic Salmonella Typhimurium (mSTM) ST34 explains its clonal expansion as an increasingly prevalent zoonotic lineage. Functional and in vivo competition experiments show that a frameshift mutation in dinB, a polymerase for translesion DNA synthesis, leads to transcriptional changes affecting flagellin gene expression and subsequent loss of the flagellin-encoding fljB, altering the requirements for gut infection. Temporal evolutionary modelling supports a role for gene loss events in a specific chronological order for mSTM ST34 expansion. Our findings reveal a stepwise pathoadaptation model underpinning clonal global spread, providing mechanistic insights relevant to forecasting future pandemics.

Journal Article↗
PubMed2025

ClinGen recuration of hearing loss-associated genes demonstrates significant changes in gene-disease validity over time.

PURPOSE: The Clinical Genome Resource (ClinGen) Hearing Loss Gene Curation Expert Panel was assembled in 2016 and has since curated 174 gene-disease relationships (GDRs) using ClinGen's semiquantitative framework. ClinGen mandates the timely recuration of all GDRs classified as Disputed, Limited, Moderate, and Strong every 2 to 3 years. METHODS: Thirty-five GDRs met the criteria for recuration within 2 years of original curation. Previous evidence was reevaluated using the latest curation guidelines, and a comprehensive literature review was performed to obtain new evidence. Recurations were approved by the Gene Curation Expert Panel and published on the ClinGen website (www.clinicalgenome.org). RESULTS: Eight of 35 GDRs (22%) changed their classification. Two Moderate and 5 Strong GDRs were upgraded to Definitive because of new case evidence. One Strong was subsumed under another Definitive GDR after evaluation of the lumping/splitting of disease entities. Twenty-seven of 35 patients remained unchanged, with little to no new evidence reported. CONCLUSION: Genes classified as Moderate and Strong were likely to build evidence and change their classification over time, whereas Limited were unlikely to gain evidence. These findings highlight the critical role of recuration in ensuring that genetic tests and research studies incorporate the most recent evidence into their efforts.

Humans↗
PubMed2026

Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes.

Biological clocks allow organisms to anticipate cyclical environmental changes, yet in high-latitude or deep-sea habitats, the diel cues that entrain these rhythms are often seasonally diminished or absent. Fishes of the order Perciformes have rapidly diversified across these arrhythmic ecosystems, raising the question of whether changes to circadian rhythms and biological clock genetic architecture are a component of their evolutionary success. Here, we used a comparative genomic approach to investigate patterns of core biological clock gene loss across 96 perciform and five outgroup species. We found widespread and lineage-specific loss in core clock genes, particularly in the convergently evolving polar and deep-sea suborders Notothenioidei and Cottoidei. This trend of clock gene loss was significantly amplified with higher-latitude species. To determine if these genomic signatures reflect a functional loss of rhythmicity, we performed metabolic phenotyping on three notothenioid species. We found a consistent lack of circadian metabolic oscillations during the late austral fall across all notothenioids, including the sub-Antarctic sister lineage to the cryonotothenioid adaptive radiation, Eleginops maclovinus. Experimental data across Perciformes, combined with suborder-wide patterns of gene loss, suggest that a release from circadian constraints occurred early in their diversification, potentially facilitating the repeated expansion of these fishes into polar and deep-sea habitats.

Animals↗
PubMed2025

Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes.

Biological clocks enable organisms to anticipate cyclical environmental changes. Some habitats, such as those at high latitudes or deep sea, experience seasonally diminished or absent diel cues upon which species entrain their circadian rhythms. Fishes of the order Perciformes have rapidly diversified and adapted to these arrhythmic ecosystems, raising the possibility that evolutionary modifications to their circadian biology contributes to their success as one of the most species-rich orders of vertebrates. Here, we used a comparative genomic approach to investigate patterns of biological clock gene loss and circadian rhythms across 33 perciform and six outgroup species. We found both widespread and lineage-specific loss and relaxed selection in core clock genes, particularly in the convergently evolving polar and deep-sea Notothenioidei and Cottioidei suborders. This trend of circadian gene loss was significantly correlated with latitude, with higher-latitude species showing greater loss. Whether these losses and relaxed selection lead to changes in circadian rhythms is unknown for most perciforms. To address this, we performed metabolic phenotyping on three notothenioid species and found no circadian metabolic oscillations during the late austral fall, including in the sub-Antarctic Eleginops maclovinus, sister to the Antarctic adaptive radiation. We propose that diminished reliance on endogenous biological clocks may be an adaptive feature that facilitates the survival and diversification of perciform fishes in polar and arrhythmic environments.

Journal Article↗
PubMed2025

Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogen Zymoseptoria tritici.

Interactions between plant pathogens and their hosts are highly dynamic and mainly driven by pathogen effectors and plant receptors. Host-pathogen co-evolution can cause rapid diversification or loss of pathogen genes encoding host-exposed proteins. The molecular mechanisms that underpin such sequence dynamics remains poorly investigated at the scale of entire pathogen species. Here, we focus on AvrStb6, a major effector of the global wheat pathogen Zymoseptoria tritici, evolving in response to the cognate receptor Stb6, a resistance widely deployed in wheat. We comprehensively captured effector gene evolution by analyzing a global thousand-genome panel using reference-free sequence analyses. We found that AvrStb6 has diversified into 59 protein isoforms with a strong association to the pathogen spreading to new continents. Across Europe, we found the strongest differentiation of the effector consistent with high rates of Stb6 deployment. The AvrStb6 locus showed also a remarkable diversification in transposable element content with specific expansion patterns across the globe. We detected AvrStb6 gene losses and evidence for transposable element-mediated disruptions. We used virulence datasets of genome-wide association mapping studies to predict virulence changes across the global panel. Genomic predictions suggested marked increases in virulence on Stb6 cultivars concomitant with the spread of the pathogen to Europe and the subsequent spread to further continents. Finally, we genotyped French bread wheat cultivars for Stb6 and monitored resistant cultivar deployment concomitant with AvrStb6 evolution. Taken together, our data provides a comprehensive view of how a rapidly diversifying effector locus can undergo large-scale sequence changes concomitant with gains in virulence on resistant cultivars. The analyses highlight also the need for large-scale pathogen sequencing panels to assess the durability of resistance genes and improve the sustainability of deployment strategies.

Ascomycota↗
PubMed2026

Nucleotide Combination Proportions Across Algae, Monocotyledons and Dicotyledons: Insights into Plant Genome Evolution.

Plant evolution started with unicellular algae, gradually evolving multicellularity and terrestrial colonization. These evolutionary events were accompanied by the interplay of chromosome polyploidization, rearrangement, gene loss, and point mutation. We counted the proportion of nucleotide combinations in the genome sequences of 64 sequenced plants, and analyzed the significant difference in these nucleotide combination proportions among algae, monocotyledons and dicotyledons. The correlation of highly significant different and no significant different nucleotide combinations was analyzed respectively. Nucleotide combinations and their reverse complementary sequence proportions were analyzed in different functional regions of the genome. These results reveal that some nucleotide combinations are subject to strict selection, and these combinations have a higher proportion in the CDS regions and lower proportion in the intergenic regions. Meanwhile, there are some nucleotide combinations that are under less selective pressure, and these combinations have a higher proportion in the intergenic regions and lower proportion in the CDS regions. Cluster analysis based on trinucleotide to octanucleotide combination proportions reveals that plant genome evolution is accompanied by clade-wide differentiation of genome-wide nucleotide composition patterns, in addition to well-documented chromosomal polyploidization, structural rearrangement and gene loss events. We analyzed the changes in the proportion of nucleotide combinations at the genome level in 64 sequenced plants, providing a new idea for studying genome evolution in the plant kingdom.

comparative genomics↗
PubMed2026

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones.

Sea anemones occupy the full depth range of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with publicly available actiniarian data. We find support for a shallow-water origin of Actiniaria through a framework that emphasizes genome-scale changes associated with habitat transitions. Most strikingly, these changes include repeated dismantling of the circadian toolkit across deep-sea lineages. In addition to convergent gene losses in photo- and temperature-regulatory genes, we find that some deep-sea lineages have experienced recurrent loss or pseudogenization of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, and Mlh3), suggesting reduced meiotic capacity in some lineages. Despite this extensive genomic erosion, deep-sea anemones exhibit molecular tuning: specific amino acid substitutions improve enzyme performance under low-temperature conditions relevant to the deep sea, while selective expansions of gene families related to neural excitability, membrane systems, and other functions may help maintain physiological performance in this environment. Functional assays in yeast indicate enhanced performance of the deep-sea variants at 4°C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

Actiniaria↗
PubMed2026

Evolutionary architecture and lineage-specific diversification of Forkhead box transcription factors in Perna viridis.

The Forkhead box (Fox) transcription factors are evolutionarily conserved regulators of development, cell cycle, and apoptosis across metazoans. This study provides the first comprehensive genome-wide analysis of the Fox gene family in the Asian green mussel (Perna viridis). We identified 28 Fox genes distributed across 10 chromosomes. Comparative analysis reveals the absence of the FoxI, FoxQ1, FoxR and FoxS subfamily, consistent with other bivalves and indicative of lineage-specific gene loss during molluscan evolution. Notably, gene duplications in the FoxAB, FoxD, FoxH, FoxN1-4, FoxQ2 and FoxQD subfamilies may reflect functional diversification associated with environmental adaptation. Exon-intron structural variability, including intron loss in several paralogues, suggests structural diversification and potential regulatory variation. Phylogenetic reconstruction confirmed the monophyly of core Fox classes while highlighting divergent expansion patterns in lophotrochozoans. Selection analyses showed strong purifying selection across duplicated Fox paralogs, supporting functional conservation after lineage-specific expansion. Gene Ontology enrichment linked Fox genes to stress response, apoptosis, and transcriptional regulation. By integrating phylogenetic, structural, and transcriptomic analyses, this study provides a genomic framework for understanding Fox gene organisation, evolution, and tissue-associated expression patterns in Perna viridis and establishes a comparative resource for future functional studies in bivalves.

Animals↗
PubMed2025

Comparative genomic analysis of Artemisia argyi reveals asymmetric expansion of terpene synthases and conservation of artemisinin biosynthesis.

Artemisia argyi, a perennial herb of the Asteraceae family, possesses significant therapeutic and economic value. We present a 7.88 Gb chromosome-level haplotype-resolved genome assembly, revealing its unique evolutionary trajectory. The karyotype (2n = 34) of A. argyi is that of an autotetraploid, which underwent gametic chromosome fusion prior to species-specific whole-genome duplication (WGD-3). The genome exhibits pronounced multivalent chromosome pairing and frequent recombination among homologous groups. Asymmetrical evolution following WGD-3 is a hallmark feature, evidenced by imbalanced allelic gene loss and widespread neofunctionalization. The terpene synthase (TPS) gene family exemplifies this pattern, having expanded through four duplication events in A. argyi. Recent tandem duplications and allelic functional differentiation have generated substantial gene functional diversity. Notably, we identified a tandem-duplicated six-copy ADS homolog (AarADS)-a key TPS gene in the artemisinin biosynthetic pathway of Artemisia annua (AanADS)-localized exclusively to a single chromosome in A. argyi. Unlike AanADS, which converts farnesyl pyrophosphate (FPP) to amorpha-4,11-diene, AarADS catalyzes FPP to α-bisabolol. Evolutionary analysis suggested that AanADS acquired its specialized function via a derived mutation in the A. annua lineage. This study elucidates the genomic evolution underpinning A. argyi's distinctive medicinal properties.

Alkyl and Aryl Transferases↗
PubMed2025

Two-Step Loss of GLUTs in the High-Metabolism Passerines.

Glucose transporters (GLUTs) play vital roles in cellular metabolism. Understanding their evolutionary dynamics in birds is essential for elucidating avian physiology and adaptation. However, the choice of gene detection method in gene family analysis may affect the conclusion. Here, we present a comprehensive investigation of methodologies and GLUT gene loss events in avian lineages, focusing on the loss of GLUT4 and GLUT8. To illustrate the effects of these methods, we first employed BUSCO-based homolog identification, calculated pairwise evolutionary distances between different species, and performed separate blastn and blastp searches to identify homologs in two groups of animals. Our analyses revealed a significant decline in blastn accuracy with increasing evolutionary distance, represented by relative divergence times. Through a more robust blastp-based gene detection pipeline, we provide evidence for the loss of GLUT genes in birds based on 58 vertebrate genomes, including 47 bird species. Our results support the reported early loss of GLUT4 in Aves. We also newly emphasize the absence of GLUT8 in passerines, potentially due to adaptation to high-sugar diets in their ancestors. These findings enhance our knowledge of avian metabolism and the evolution of GLUT genes.

Animals↗
PubMed2025

Golgi_traff phylogeny reveals ancient eukaryotic genes with recent surprises: replication and diversification of HID1 domain-containing protein unique to Schizosaccharomyces.

Golgi_traff is a Pfam clan containing two members, Dymeclin (DYM) and HID1 domain-containing protein (HID). Interrogation of over 900 eukaryotic genomes with sequence models showed that both are ancient eukaryotic genes, which have exhibited different paths of gene loss, including from major taxonomic groups. For example, the Metazoa have both genes, whereas the Viridiplantae and Dikarya have lost HID and DYM, respectively. A unique replication event occurred within the genus Schizosaccharomyces in that all sequenced species possess three HID-encoding paralogs, whereas its nearest fungal relatives and other eukaryotes are almost exclusively monogenic. A phylogenetic analysis of yeasts revealed that the Golgi-resident paralog Human ortholog 3 (SPAC17A5.16) is more similar to the HID of other yeasts than to its paralogs. Transmission electron microscopy revealed that the SPAC17A5.16 mutant lacks a stacked Golgi apparatus (GA) form, suggesting a role in maintaining GA structure. Altered proliferation of the SPAC17A5.16 mutant in response to GA disrupting chemical agents indicated a perturbation of GA-related functions. Structural models suggest SPAC17A5.16 has a long, disordered N-terminal region that may facilitate anchoring to GA membranes. A modification to Schizosaccharomyces HID nomenclature is proposed to reflect their evolutionary and functional characteristics. The potential of the Golgi_traff clan to serve as a model for the diversification of protein function according to the concepts of sub/neofunctionalization is discussed.

Schizosaccharomyces↗
PubMed1979

Control of transcription and translation by low molecular weight peptides (deprimerones) from chromatin and poly(A)-messenger RNA. Implication in the mechanism of carcinogenesis.

Poly(A)-mRNA isolated by phenol/chloroform extraction of rat liver polysomes, subtilism digestion, and poly(U)-Sepharose chromatography, contains a low molecular weight (approx. 1000) peptidic fraction. The peptides were extracted from a poly(A)-mRNA fraction by treatment with 80% ethanol; after ethanol evaporation they were purified on a Sephadex G-25 column and high-performance liquid chromatography on muBondapak C18. The isolated peptides were analyzed by cellulose gel thin-layer chromatography, high-pressure liquid chromatography and their amino acid composition was determined. They were compared with a chromatin peptidic fraction isolated from calf thymus nucleic by affinity chromatography on DNA-cellulose or on Sephadex G-25 column. Both groups of peptides from chromatin and from poly(A)-mRNA bind to the purified DNA thereby increasing its melting point; they significantly inhibit DNA transcription and RNA translation in reconstituted cell-free, peptide-free systems. It is suggested that these peptides are endogenous natural regulatory substances controlling gene expression in eucaryotic cells. We propose to name these regulatory peptides 'deprimerones' (from Latin 'deprimere') and describe various fractions of them as chromatin deprimerones, messenger deprimerones, gene deprimerones (for specific genes). Loss or decreased level of these deprimerones during the promotion of carcinogenesis is responsible for uncontrolled gene expression observed in cancer.

Animals↗
PubMed2025

Genomic evolution of EGF-CFC genes in deuterostomes.

BACKGROUND: EGF-CFC proteins are a bilaterian innovation, but they are best known for their roles in Nodal signaling during gastrulation and left-right patterning in vertebrates. Species with multiple family members show evidence of functional specialization. For example, in mouse, Cripto is required for gastrulation, whereas CFC1 is involved in left-right patterning. However, members of the EGF-CFC family across model organisms exhibit limited sequence conservation beyond the EGF-CFC domain, posing challenges for determining their evolutionary history and functional conservation. RESULTS: In this study, we describe the evolutionary history of the EGF-CFC family of proteins across several branches of deuterostomes, with a particular focus on vertebrates. We trace the EGF-CFC gene family from a single gene in the deuterostome ancestor through its expansion and functional specialization in tetrapods, and subsequent gene loss and translocation in eutherian mammals. Mouse Cripto and CFC1, zebrafish Tdgf1, and each Xenopus EGF-CFC gene (Tdgf1, Tdgf1.2 and Cripto.3) are all descendants of the ancestral deuterostome Tdgf1 gene. CONCLUSIONS: We propose that subsequent to EGF-CFC family expansion in tetrapods, Tdgf1B (Xenopus Tdgf1.2) acquired specialization in the left-right patterning cascade, and then after its translocation in eutherians to a different chromosomal location, CFC1 has maintained that specialization.

Animals↗
PubMed2026

Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces.

Microbial secondary metabolites have been recognized and utilized for nearly a century. Nevertheless, the eco-evolutionary mechanisms governing their distribution among microorganisms remain largely unresolved. In this study, we examined intraspecific interactions within Streptomyces albidoflavus and identified a strain exhibiting potent antagonistic activity against conspecifics. This "killer" phenotype was attributed to the production of kosinostatin, a hybrid aromatic polyketide antibiotic. Evolutionary genomic analyses provided strong evidence that the kosinostatin biosynthetic gene cluster was horizontally acquired in S. albidoflavus over a relatively short evolutionary timescale, a finding consistent with its sparse distribution within this species, across the genus Streptomyces, and even throughout the phylum Actinomycetota. Using microcosm assays, we demonstrated that the kosinostatin producer outcompeted sensitive conspecifics in liquid culture but not in soil, indicating that environmental context plays a key role in altering the fitness benefits of this cluster. Moreover, the competitive advantage was observed only in the presence of sensitive strains, revealing a trade-off between fitness benefits and metabolic costs. These results highlight the role of context-dependent selection in shaping the evolutionary persistence of the kosinostatin cluster. The current distribution pattern of this cluster in S. albidoflavus likely results from a dynamic interplay of intraspecific horizontal gene transfer, vertical inheritance, and recurrent gene loss. Overall, our findings establish an eco-evolutionary framework that explains the rarity of a potent antibiotic gene cluster in Streptomyces, illustrating how environmental constraints, fitness trade-offs, and gene flux collectively orchestrate the biosynthetic architecture of Streptomyces species.

Streptomyces↗
PubMed2025

The genomic origin of the unique chaetognath body plan.

The emergence of animal phyla, each with their unique body plan, was a rapid event in the history of animal life, yet its genomic underpinnings are still poorly understood1. Here we investigate at the genomic, regulatory and cellular levels, the origin of one of the most distinctive animal phyla, the chaetognaths, whose organismal characteristics have historically complicated their phylogenetic placement2,3. We show that these characteristics are reflected at the cell-type level by the expression of genes that originated in the chaetognath lineage, contributing to adaptation to planktonic life at the sensory and structural levels4. Similarly to other members of gnathiferans (which also include rotifers and several other microscopic phyla)5,6, chaetognaths have undergone accelerated genomic evolution with gene loss and chromosomal fusions7,8. Furthermore, they secondarily duplicated thousands of genes9,10, without evidence for a whole-genome duplication, yielding, for instance, tandemly expanded Hox genes, as well as many phylum-specific genes. We also detected repeat-rich highly methylated neocentromeres and a simplified DNA methylation toolkit that is involved in mobile element repression rather than transcriptional control. Consistent with fossil evidence11,12, our observations suggest that chaetognaths emerged after a phase of morphological simplification through a reinvention of organ systems paralleled by massive genomic reorganization, explaining the uniqueness of their body plan.

Animals↗