Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae.
Sudianto E, Baurain D, Cornet L
Genome Biol Evol · 2026 Jun · PMID 42175760 · Full text
Gloeobacterales occupy a key phylogenetic position among cyanobacteria and are distinguished by the absence of thylakoid membranes. Using comparative genomics and phylogenetic analyses, we show that horizontal gene trans...
Gloeobacterales occupy a key phylogenetic position among cyanobacteria and are distinguished by the absence of thylakoid membranes. Using comparative genomics and phylogenetic analyses, we show that horizontal gene transfer has played a major role in shaping the central carbon metabolism of this lineage. In Gloeobacteraceae-one of the two families within the order-we identify a complete ribose ATP-synthase binding cassette importer and associated metabolic enzymes that enable ribose uptake and assimilation into central carbon metabolism alongside photosynthesis, indicative of a photomixotrophic lifestyle. Beyond ribose utilization, their central carbon metabolism exhibits a mosaic architecture shaped by the integration of foreign genes into the Calvin-Benson-Bassham cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway. Uniquely, these genes appear to have been acquired through multiple independent transfer events, as reflected by their dispersed genomic locations and diverse bacterial donors, including other cyanobacteria and Pseudomonadota. These findings highlight Gloeobacterales as a dynamic lineage that continues to adapt and evolve through metabolic innovation and the assimilation of foreign genes into its genomes.
Evolution of Gene Expression Across Functional Regions of the Mouse Placenta.
Rodriguez-Caro F, Moore EC, Slanger A … +1 more , Good JM
Genome Biol Evol · 2026 May · PMID 42175731 · Full text
The eutherian placenta exhibits rapid morphological evolution and is a hotspot for the emergence of reproductive incompatibilities between closely related species. These evolutionary patterns are thought to be a conseque...
The eutherian placenta exhibits rapid morphological evolution and is a hotspot for the emergence of reproductive incompatibilities between closely related species. These evolutionary patterns are thought to be a consequence of rapid divergence in gene expression driven by maternal-fetal conflict over resource allocation. However, it remains unclear how the diversity of placental functions shapes gene specialization and expression divergence. We generated genome-wide gene expression and DNA methylation data from fetal and maternal placental tissues of three closely related mouse lineages (Mus musculus musculus, M.'m.'domesticus, M. spretus) and integrated single-cell expression data to investigate how tissue specialization influences gene expression evolution in the rodent placenta. Comparisons among placental regions within M.'m.'musculus revealed significant differences in patterns of functional enrichment, imprinting, and X-linked expression across placental layers. The labyrinth zone, the primary site of nutrient exchange, showed strong enrichment for parent-of-origin expression of both autosomal and X-linked genes. Cross-species comparisons of gene expression within each placental layer revealed increased expression level divergence at the maternal-fetal interface. We also identified a subset of genes with maternally biased expression that are spatially associated with the maternal-fetal interface. Parent-of-origin DNA methylation was dominated by epigenetic modification of the maternal genome and interspecific comparisons of parent-of-origin expression revealed overall conservation punctuated by changes in imprinting status of two genes. These findings unveil important links between core elements of placental biology and the evolution of placental gene expression, demonstrating how tissue specialization has influenced parent-of-origin effects and interspecific expression divergence.
Evolutionary Analysis of Trehalose Breakdown Pathways.
Muthu G G, Laxman S, Seshasayee ASN
Genome Biol Evol · 2026 Jun · PMID 42175661 · Full text
Trehalose is a widely prevalent disaccharide that acts as a cellular stress protectant and functions as an energy source that enters central carbon metabolism when broken down. The evolution and distribution of trehalose...
Trehalose is a widely prevalent disaccharide that acts as a cellular stress protectant and functions as an energy source that enters central carbon metabolism when broken down. The evolution and distribution of trehalose breakdown pathways across kingdoms of life is not well studied, and therefore the ability of different organisms to consume trehalose as a carbon source is unknown. In this study, we build a comprehensive evolutionary analysis of the four known trehalose breakdown pathways-trehalase (acid, neutral, glycosyl hydrolase 15), trehalose phosphorylases (TP, treP), and trehalose specific phosphotransferases (PTS), by studying their distributions across ∼3,800 prokaryotic and eukaryotic genomes. Our study suggests the presence of trehalase in the last eukaryotic common ancestor, and reveals near-universal presence of trehalase in eukaryotes, except in all birds where trehalase was lost in the first bird ancestor. Fungi alone retain additional TPs in addition to trehalase. In contrast, while trehalose breakdown in prokaryotes is highly sporadic, it can occur via multiple, independently evolved pathways, including trehalase, the trehalose-specific PTS and TP. Finally, we observe that a subset of fast-growing Gammaproteobacteria retain the trehalose specific PTS, the loss of which reduces growth in Escherichia coli. Overall, our findings uncover the evolutionary landscape of trehalose breakdown, and use of this versatile disaccharide as an energy reserve in different kingdoms of life.
Genomic Patterns of Parallel Divergence Across Demographically Heterogeneous Stickleback Populations in Eastern Canada.
García-Elfring A, Paccard A, Barrett RDH
Genome Biol Evol · 2026 May · PMID 42175655 · Publisher ↗
The threespine stickleback (Gasterosteus aculeatus) is a key model in evolutionary genetics, particularly for studies of parallel evolution, yet most genomic insights derive from populations on the west coast of North Am...
The threespine stickleback (Gasterosteus aculeatus) is a key model in evolutionary genetics, particularly for studies of parallel evolution, yet most genomic insights derive from populations on the west coast of North America and in Europe. Here, we use restriction site-associated DNA sequencing (RAD-seq) of pooled samples to examine genomic differentiation between marine and freshwater stickleback populations from Atlantic Canada. Our analyses reveal substantial heterogeneity in the extent and genomic distribution of marine-freshwater differentiation, with some freshwater populations showing strong divergence consistent with long-term isolation and drift, and others exhibiting patterns consistent with ongoing gene flow and admixture. Despite this demographic variation, we identify genomic regions that are repeatedly differentiated between marine and freshwater habitats, including loci near dopamine receptor genes (Drd4a and Drd2l). Gene ontology analyses of candidate regions show enrichment for functions related to nervous system development and dopamine receptor activity. Together, these results indicate that freshwater-associated genomic differentiation in Atlantic Canadian stickleback occurs across contrasting demographic contexts and suggest a potential role for neurological and behavioural pathways in adaptation to freshwater environments.
On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction.
Kant P, Petersen B, Sicheritz-Pontén T … +1 more , Kondabagil K
Genome Biol Evol · 2026 May · PMID 42171474 · Full text
The role of bacteriophages in spreading antimicrobial resistance genes (ARGs) has been debated for over a decade. Several questions regarding the ARG dissemination potential of bacteriophages remain. For example, do phag...
The role of bacteriophages in spreading antimicrobial resistance genes (ARGs) has been debated for over a decade. Several questions regarding the ARG dissemination potential of bacteriophages remain. For example, do phages frequently carry ARGs? Besides generalized transduction (GT), could specialized transduction (ST) play an essential role in the spread of ARGs? To address these questions, we thoroughly analyzed the available phage genomes, viromes, temperate phages, and prophage sequences for the presence of all known ARGs and their genomic context. Out of the 38,861 phage genome sequences we analyzed, 82 phages were found to possess 141 ARGs in their genomes. Interestingly, a few of the Streptococcus phages were found to carry an entire ARG cluster with four or more genes. An uncharacterized Caudoviricetes phage was found to possess the complete vancomycin operon. In literature, the role of ST in phage-based ARG dissemination is often overlooked. Based on the presence of lysogenic markers, the terminal location of ARGs on phage genomes, and ARG clusters transferred to phages, we suggest that ARGs are predominantly acquired from pathogenic hosts by temperate phages via ST. These findings indicate that, in addition to GT, ST can also play a crucial role in phage-based ARG dissemination. Our study also suggests that the acquisition of ARGs by phages is sporadic. Overall, we propose that phage-mediated gene transfer is governed by a complex interplay of gene transfer bottlenecks and microenvironmental parameters, such as microbial density, diversity, and external stress, in addition to phage properties.
Genomic Footprints of Selfing, Introduction History, and Long-Distance Dispersal in an Invasive Alien Plant.
Sánchez-García R, Green AJ, Ortiz MA … +9 more , García C, Hortas F, Reynolds C, Rowntree J, Serrão EA, Tomasson L, Tremetsberger K, van Leeuwen CHA, Ortego J
Genome Biol Evol · 2026 Jun · PMID 42171002 · Full text
Biological invasions are natural experiments for studying the evolutionary and ecological processes underlying colonization success and range expansion. Using genome-wide data-generated via genotyping-by-sequencing (GBS)...
Biological invasions are natural experiments for studying the evolutionary and ecological processes underlying colonization success and range expansion. Using genome-wide data-generated via genotyping-by-sequencing (GBS) from 30 populations spanning Europe and South Africa-we investigated the colonization history and successful spread of the invasive buttonweed Cotula coronopifolia, an annual plant introduced into Europe from South Africa about 300 years ago. Our analyses identified three major lineages in Europe distributed across the continent, often co-occurring without evidence of admixture. Phylogenomic dating revealed that these lineages diverged > 2,000 years ago-well before the earliest European records-suggesting divergence within the native range and either multiple introductions or a single introduction with multiple lineages. Mating-system inference shows that reproduction occurs primarily via self-fertilization (∼70% on average), although outcrossing predominates in some populations, revealing a facultative mating system. This high selfing rate has led to extremely low heterozygosity in most populations and a strong genetic structure. Genetic clustering also revealed admixed individuals resulting from rare inter-lineage outcrossing; comparisons of empirical and simulated data indicate that increased diversity after sporadic admixture events decays rapidly under subsequent selfing. Both the introduction history and long-distance dispersal facilitated by waterbirds likely explain the scattered distribution of lineages across Europe. Altogether, these results illustrate Baker's "ideal weed" concept, highlighting the role of a flexible mating system in providing reproductive assurance during colonization and showing how predominant selfing can shape the genomic landscape of an invasive species.
Population Structure of the Jewel Scarab Chrysina gloriosa.
Sylvester T, Hjelmen CE, Thompson MJ … +5 more , Blackmon LT, Alfieri JM, Hoover Z, Esfandani T, Blackmon H
Genome Biol Evol · 2026 Jun · PMID 42159226 · Full text
The sky-island mountain ranges of the southwestern United States offer a natural setting for examining how climate and geography impact population structure and gene flow. The jewel scarab, Chrysina gloriosa, is a charis...
The sky-island mountain ranges of the southwestern United States offer a natural setting for examining how climate and geography impact population structure and gene flow. The jewel scarab, Chrysina gloriosa, is a charismatic beetle restricted to high-elevation habitats in these mountains, where isolation and environmental change may be driving population divergence. We used low-coverage whole-genome resequencing and species distribution modelling to study population structure, gene flow, and demographic history across five mountain ranges in Arizona and West Texas. Our results indicate strong genetic differentiation among most populations, with recent gene flow detected only between two neighboring ranges, possibly through male-mediated dispersal. Demographic analyses reveal a decline in effective population size following late Pleistocene climate shifts, consistent with habitat contraction inferred from paleo-vegetation records. Future climate projections suggest further habitat loss and increasing isolation. Together, these results show how past and ongoing climatic changes have and continue to shape population structure in C. gloriosa, with important implications for its long-term evolutionary potential. These findings mirror patterns documented across sky-island taxa globally, supporting a general model in which climate-driven habitat dynamics and dispersal limitation interact to generate recurrent cycles of population fragmentation, genetic erosion, and demographic instability in montane systems.
Chromosome-Level Reference Genome of the Beach False Foxglove, Agalinis fasciculata (Orobanchaceae).
Pezzi PH, Latvis M
Genome Biol Evol · 2026 May · PMID 42136183 · Full text
Orobanchaceae is the largest family of parasitic plants, encompassing a full spectrum of parasitic strategies, ranging from autotrophic to holoparasitic. Agalinis is a genus of facultative hemiparasites comprising about...
Orobanchaceae is the largest family of parasitic plants, encompassing a full spectrum of parasitic strategies, ranging from autotrophic to holoparasitic. Agalinis is a genus of facultative hemiparasites comprising about 70 species distributed throughout the Americas, including several endemic and rare taxa. Agalinis fasciculata, the beach false foxglove, is a widely distributed species across southeastern North America. Here, we use PacBio HiFi, Omni-C, and RNA-seq data to generate the first high-quality reference genome for the genus. The nuclear genome is 2.29 Gb in size, with most sequences anchored to 14 pseudochromosomes and an N50 of 162 Mb. BUSCO analyses indicate high completeness (98.4%). Structural genome annotation identified 34,133 protein-coding genes and 39,266 transcripts, most of which have at least one functional annotation. We have also assembled the plastid and mitochondrial genomes into complete circular molecules. We further examined genetic diversity and demographic history in A. fasciculata, revealing low genome-wide heterozygosity and evidence of inbreeding. This reference genome is an important resource for understanding the evolutionary history of the genus and the evolutionary patterns of parasitism within Orobanchaceae.
Inferring Patterns of Purifying, Positive, and Balancing Selection in the Coppery Titi Monkey (Plecturocebus cupreus) Utilizing a Well-Fit Evolutionary Baseline Model.
Soni V, Versoza CJ, Terbot JW … +4 more , Spatola GJ, Bales KL, Pfeifer SP, Jensen JD
Genome Biol Evol · 2026 May · PMID 42136161 · Full text
Despite the coppery titi monkey (Plecturocebus cupreus) being a model system for the study of neurodevelopment and behavior, the evolutionary forces shaping observed levels and patterns of genetic variation in the specie...
Despite the coppery titi monkey (Plecturocebus cupreus) being a model system for the study of neurodevelopment and behavior, the evolutionary forces shaping observed levels and patterns of genetic variation in the species have remained poorly studied. In order to illuminate the pervasive effects of purifying and background selection, we have fit a distribution of fitness effects of newly arising exonic mutations, utilizing patterns of polymorphism and divergence based on a recently published high-quality genome assembly. To further characterize episodically acting selective processes, we additionally performed the first whole-genome scans for recent positive and balancing selection in this species, reducing false-positive rates by incorporating the demographic history of the population into an evolutionary null model. These scans identified a small number of biomedically relevant genes with strong statistical support for having experienced recent selective sweeps or long-term balancing selection. In addition, we identified four genomic deletions bearing the signatures of balancing selection. Taken together, this study provides the first insights into patterns of persistent and episodic selective processes in this species.
Genus-wide Homologous Recombination of Tail Fibers Maintains Tailocin Diversity in Pectobacterium.
Pardeshi LA, Kupczok A, de Ridder D … +2 more , Smit S, van der Lee TAJ
Genome Biol Evol · 2026 May · PMID 42126071 · Full text
Due to their ability to kill closely related strains, phage tail-like bacteriocins, also called tailocins, play an important role in shaping bacterial communities. One such tailocin, called carotovoricin, is also known t...
Due to their ability to kill closely related strains, phage tail-like bacteriocins, also called tailocins, play an important role in shaping bacterial communities. One such tailocin, called carotovoricin, is also known to be present in the Pectobacterium genus. However, little is known about its evolutionary dynamics and the scope of impact on species interactions in this genus. To investigate the diversity and evolution of carotovoricin, we performed a genus-wide, phylogenetically-structured pangenome study. This analysis inferred that the gene cluster responsible for carotovoricin biosynthesis is conserved across the genus and is located in the same gene neighborhood in all the species. Within the carotovoricin cluster, the tail fiber genes, which determine the host range specificity, exhibit high variability and discordance with the species phylogeny. We show evidence for an evolutionary mechanism involving recombination-mediated exchange of these tail fiber loci across the entire Pectobacterium genus, which complements the previously known mechanism for DNA sequence inversion to maintain tailocin polymorphism at the population level. In addition, the ability to exchange tail-fiber loci in a highly targeted and genus-wide manner could influence the community dynamics in nutrient rich environments such as infected plant tissues. In conclusion, the strong signal for carotovoricin retention and ability to exchange tail fibers indicates that it significantly contributes to the community interactions of the Pectobacterium phytopathogens.
In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee.
Okamoto AS, Coveney CR, Ganapathee DS … +1 more , Capellini TD
Genome Biol Evol · 2026 May · PMID 42119152 · Full text
Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal modifications underpin key events in human evolution, enabling our species...
Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal modifications underpin key events in human evolution, enabling our species to walk upright, manipulate tools with precision, and support enlarged brains. Identifying the genomic changes that underlie these features remains an outstanding challenge due to the substantial number of differences between the human and chimpanzee genomes. To identify human-chimp sequence differences that modulate gene expression in the developing postcranial skeleton, we used a massively parallel reporter assay to screen the human and chimp versions of 70,000 regulatory elements present in the prenatal skeletal template for differential activity. After testing our library in two cartilage (CHON002 and T/C-28a2) and one control cell line (K562), we identify 30,736 regions (45.2%) with activity in our assay. Of the active regions, we find that 11,542 (37.6%; or 17% of the entire pool) regions exhibited differential activity between the human and chimpanzee. We find that human ancestor quickly evolved regions were predictive of differential activity while human accelerated regions were not and both sets failed to predict the magnitude of effect, unlike the total number of base pair differences between species, which was weakly correlated with effect size. These findings are consistent with a polygenic model of human skeletal evolution based on widespread regulatory changes distributed across thousands of elements rather than concentrated effects at a few key loci.
The Nuclear and Mitochondrial Genomes of the Lined Rockskipper, Istiblennius lineatus (Teleostei: Blenniidae).
Valencia-Cárdenas VM, Kulikov N, Contreras-Martín R … +7 more , Ruiz-Ruano FJ, Ben Hamadou A, Greve C, Estekani S, Vaz DFB, Ord TJ, Irisarri I
Genome Biol Evol · 2026 May · PMID 42117780 · Full text
We generated nuclear and mitochondrial chromosome-scale genome assemblies for Istiblennius linneatus (Valenciennes, 1836), an amphibious fish of the family Blenniidae. The assemblies were produced from Pacific Bioscience...
We generated nuclear and mitochondrial chromosome-scale genome assemblies for Istiblennius linneatus (Valenciennes, 1836), an amphibious fish of the family Blenniidae. The assemblies were produced from Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read data and Arima high-throughput chromosome conformation capture (Hi-C) technology. The nuclear genome assembly is 643.23 Mb in size, with a scaffold N50 of 24 Mb, a contig N50 of 6.39 Mb, and a GC content of 43.34%. We reconstructed the 24 pseudochromosomes expected from karyotype studies, which account for 86.95% of the genome assembly. After manual assembly curation, the obtained genome assembly is highly complete (97.3% BUSCO completeness) and free of haplotypic duplication and contaminations. The genome was annotated using direct RNA-seq and protein homology evidence, obtaining 27,357 gene models (95.4% BUSCO completeness). Genome size and macro-synteny is overall conserved with other available combtooth blenny genomes. The mitochondrial genome is 16.5 kb in length and has the gene content and order typical of the family and of most vertebrates. These new genomic resources can provide new insights into the ecology and evolutionary history of Istiblennius.
Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite.
Brann T, Souza de Oliveira F, Iriarte A … +1 more , Protasio AV
Genome Biol Evol · 2026 May · PMID 42102165 · Full text
In eukaryotes, horizontal gene transfer (HGT) often involves transposable elements (TEs), host-parasite relationships, aquatic environments, or any of them combined. Horizontal transfer of transposable elements is both i...
In eukaryotes, horizontal gene transfer (HGT) often involves transposable elements (TEs), host-parasite relationships, aquatic environments, or any of them combined. Horizontal transfer of transposable elements is both impactful, owing to the subsequent transposition burst, and insightful, providing information on organisms' evolutionary history. The flatworm Schistosoma mansoni is a human parasite with two free-living aquatic stages (intercalated between a definitive human host and intermediate snail host) and has a sizable TE content. We aimed to identify and characterize potential instances of HGT leveraging new genomic resources available. Using the latest chromosome-scale genome assembly and available TE sequences for the S. mansoni genome, we identify that two TEs, named Perere-3 and Sr3, are putatively horizontally transferred. We demonstrate the presence of these TEs in the genomes of Schistosoma spp. intermediate hosts, most likely explained by HGT. Perere-3/Sr3 were also found across a wide range of additional organisms not susceptible to schistosome infection, including turtles, fish, and other mollusks. We propose that the patchy distribution of Perere-3/Sr3 across the phylogenetic tree is best explained by HGT. Our synonymous substitution calculations further support HGT, as divergence between schistosome and snail TE sequences is markedly lower than that observed for conserved orthologous genes. We propose that HGT is likely linked to schistosomes' parasitic nature as several snail species sharing the elements are susceptible to infection. However, the rationale for the presence of Perere-3/Sr3 in species beyond this relationship is unknown.
Genome of Facultatively Parthenogenetic Harvester (Opiliones) Indicates Frequent Mitonuclear Sequence Transfer and Novel Full-Length Insertions.
Stellwagen SD, Burns M
Genome Biol Evol · 2026 May · PMID 42100827 · Full text
Facultative parthenogenesis and intrapopulation mixed ploidy (where individuals with differing ploidy exist within the same area) are rare in animals. However, these unique characteristics allow opportunities to investig...
Facultative parthenogenesis and intrapopulation mixed ploidy (where individuals with differing ploidy exist within the same area) are rare in animals. However, these unique characteristics allow opportunities to investigate the relationship between sexual modality and genome structure. We have completed a genome assembly of the Japanese harvester ("daddy-longlegs") Leiobunum manubriatum, a species that reproduces sexually and asexually and has mixed diploid and tetraploid populations. We combined Oxford Nanopore's MinION long-read sequencing platform with Dovetail Hi-C scaffolding to assemble the haploid genome for the diploid race, which is approximately 336 Mbp after collapsing heterozygous sequence. The assembly's completeness was measured using BUSCOs from Arthropoda (complete: 97.7%). We also searched raw sequence reads and the draft genome for nuclear mitochondrial DNA (numt) sequences. While only one complete mitochondrial genomic transfer was found in the draft genome, there are at least 12 complete numts across nine reads within the raw sequencing data that were collapsed during the assembly process. The genome of the L. manubriatum diploid race is a valuable resource not only for opilionid research but also for facilitating studies investigating the evolution of their unique reproductive mode and mixed ploidy. To our knowledge, this is the first published genome of a wild-derived facultative parthenogen. Future work will leverage this resource in comparative genomics and transcriptomics of L. manubriatum to understand the connection between ploidy and sexual strategy.
Population-level Variability in Genome-wide Repressive Histone Marks in a Fungal Wheat Pathogen.
Nanchira Abraham L, Sampaio AM, Bhattacharyya S … +2 more , Moser Tralamazza S, Croll D
Genome Biol Evol · 2026 May · PMID 42099281 · Full text
Epigenetic modifications influence the expression of phenotypic traits by modulating gene expression and responses to environmental cues. In plant pathogens, the expression of virulence-associated genes is known to be re...
Epigenetic modifications influence the expression of phenotypic traits by modulating gene expression and responses to environmental cues. In plant pathogens, the expression of virulence-associated genes is known to be regulated by epigenetic modifications and is considered a key adaptation for pathogens. Gene expression variation within pathogen species is regulated by extensive cis-regulatory polymorphism and insertion activities of transposable elements. However, whether pathogens vary in epigenetic profiles among members of the same species remains largely unexplored. Here, we focus on the major fungal wheat pathogen Zymoseptoria tritici and establish histone methylation profiles for 45 isolates of an extensively characterized wheat field population. We analyzed the facultative heterochromatin mark H3K27me3, thought to regulate effector and gene cluster loci in the genome. H3K27m3 coverage was increased in transposable element-rich regions, with newly inserted retrotransposons contributing to epigenetic variation among pathogen genotypes. Nearly 20% of all genes showed within-population variation in H3K27me3 marks, which likely contributes to the substantial within-population variation in gene expression. Effector candidate genes and members of gene clusters showed higher than average H3K27me3 variation. Our study provides among the first insights into intra-species epigenetic variation of a fungal pathogen and opens avenues to recapitulate epigenetic mechanisms of pathogen adaptation.
Comparative Transcriptomics Reveals an Extracellular Worm Argonaute as an Ancestral Regulator of LTR Retrotransposons.
Martinez-Ugalde I, Neophytou K, Villagrana-Pacheco Y … +9 more , Orrego Durañona A, Stevens L, Du X, Bancroft R, Hall JL, Pedersen AB, Blaxter M, Buck AH, Abreu-Goodger C
Genome Biol Evol · 2026 May · PMID 42099280 · Full text
Safeguarding the genome from non-self-elements is essential for development, reproduction, and aging. One of the major threats to genomic integrity is transposable elements (TEs), which can be post-transcriptionally sile...
Safeguarding the genome from non-self-elements is essential for development, reproduction, and aging. One of the major threats to genomic integrity is transposable elements (TEs), which can be post-transcriptionally silenced through small RNAs (sRNAs) and argonaute proteins. Recent work suggests TE-derived sRNAs may also act as virulence factors in host-pathogen interactions. During infection, the intestinal parasite Heligmosomoides bakeri secretes a single argonaute protein (exWAGO) and a wide variety of TE-derived sRNAs. Although exWAGO is highly expressed, conserved, and secreted by parasitic nematodes, its function and sRNA guide preference remain unclear. Using comparative transcriptomics of the sRNAs bound to exWAGO within parasites of rodents, livestock, and humans, and its orthologs in C. elegans, we found that exWAGO is capable of loading sRNAs produced from all classes of TEs in addition to some protein-coding and noncoding transcripts. However, our results suggest that the ancestral endogenous function of exWAGO was likely linked to LTR retrotransposon regulation. To understand how this relates to potential extracellular functions of exWAGO, we also examined the sRNAs bound to exWAGO secreted by H. bakeri in both vesicular and nonvesicular forms. Extracellular exWAGO preferentially loads sRNA guides derived from nonautonomous and fragmented LTRs, suggesting the existence of adaptable reservoirs of regulatory sRNAs with potential roles in cross-species RNA communication. Together, our results show that exWAGO is part of an evolutionarily conserved pathway for LTR retrotransposon regulation, while preferentially utilizing degenerated elements as sources of secreted sRNAs.
Reference Genome Assembly of a Tetraploid Accession of the Tuber Crop Tropaeolum tuberosum.
Ruiz-Mateus D, Scheffler I, Márquez-Cardona MDP … +3 more , Greb T, Terán W, Hunziker P
Genome Biol Evol · 2026 May · PMID 42090564 · Full text
Tropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance, and adaptation to high-altitude environments. Despite its contribution to food security and sustainab...
Tropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance, and adaptation to high-altitude environments. Despite its contribution to food security and sustainable agriculture, it remains an underutilized species with scarce genomic resources, limiting genetic and functional studies. To address this gap, we generated a reference genome assembly for a European ex situ tetraploid accession of T. tuberosum using PacBio HiFi sequencing. The assembly spans 1.3 Gb in 1,805 contigs (contigs N50 = 32.2 Mb, longest contig = 60 Mb) and recovers 87% of the estimated genome size. We assessed assembly completeness and accuracy using Benchmarking Universal Single-Copy Orthologs, which detected 98.5% complete genes (21.7% single-copy, 76.8% duplicated), 0.7% fragmented, and 0.7% missing, demonstrating near-complete gene space recovery consistent with a high-quality tetraploid genome. To evaluate transferability, we resequenced a field-collected Colombian genotype of economic relevance using Oxford Nanopore technology. Read mapping showed 99.7% of primary alignments to the reference (weighted mean coverage = 16.4×, 96.1% at ≥5×), confirming broad sequence conservation between accessions and validating the suitability of the ex situ reference as an anchor for in situ germplasm. Repetitive elements accounted for 71.3% of the genome. Using ANNEVO, we annotated 56,354 high-confidence protein-coding genes, achieving 98.3% complete BUSCOs, a PSAURON score of 97.2, and 90.5% taxonomic consistency with the rosid lineage (OMArk). This high-quality reference genome establishes a foundational resource for comparative genomics, population genomics, and functional analyses on T. tuberosum, supporting future breeding and conservation of this important food resource.
Recurrent Modular Assembly Drives Independent Origins of Group II Introns Encoding LAGLIDADG Homing Endonucleases.
Liu F, Jin S, Du Q
Genome Biol Evol · 2026 May · PMID 42090559 · Full text
Group II introns are catalytic RNAs that typically mobilize with intron-encoded reverse transcriptase/maturase (RT/M) proteins, yet a small subset encodes LAGLIDADG homing endonucleases (LHEs). The evolutionary mechanism...
Group II introns are catalytic RNAs that typically mobilize with intron-encoded reverse transcriptase/maturase (RT/M) proteins, yet a small subset encodes LAGLIDADG homing endonucleases (LHEs). The evolutionary mechanisms underlying this atypical RNA-protein association remain poorly understood. Here, we analyze 753 LHE-encoding group II introns (group II-LHE introns) from green algae, fungi, and bacteria to investigate their origins and structural diversification. Our comparative analyses reveal that these introns are distributed across four deeply divergent RNA backbone subclasses (IIA1, IIB1, IIB2, and IIC) and form 13 lineage-specific intron families. Secondary-structure reconstruction reveals a conserved catalytic core together with extensive family-specific remodeling, including variable LHE insertion sites, recurrent loss of branch-point adenosine, and differential retention of exon-recognition elements. Phylogenetic incongruence between the RNA backbone and LHE phylogenies supports multiple independent acquisitions rather than descent from a single ancestral composite element. These results demonstrate that LHE modules have been repeatedly recruited onto distinct group II intron scaffolds, highlighting recurrent modular assembly as a key mechanism in the evolution of RNA-protein mobile elements. Our study provides a unified framework for understanding the origin, diversification, and modular evolution of LHE-encoding group II introns.
Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii).
Tracy CB, Arias CF, Tysall E … +4 more , Hoeppner MP, McMillan WO, Puebla O, Bernal MA
Genome Biol Evol · 2026 May · PMID 42060844 · Full text
The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed fol...
The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed following the uplift of the CAI, including damselfishes of the Pomacentridae family. However, to date few studies have explored the genomic differences among trainsisthmian species in the Pacific and Atlantic Oceans. In this study, we present genome assemblies for the transisthmian species pair consisting of the Sergeant Major Abudefduf saxatilis (Tropical Atlantic) and the Panamic Sergeant Major Abudefduf troschelii (Tropical Eastern Pacific) derived from PacBio long-read sequencing. The new genomes are near-chromosome level, and among the highest-quality genomes currently available for coral reef fishes. We show that large structural variants distinguish the two species, including a nine-megabase inversion in linkage group (putative chromosome) six. Additionally, we show through an analysis of demographic history that alleles within the two genomes have different coalescence time distributions, which may be due to different effective population sizes, population structures, and/or selection regimes in the two oceans. Finally, we highlight gene families that were significantly expanded or contracted between A. troschelii and A. saxatilis. Some of these are related to the environmental differences between the two oceans, including gamma crystallin M (crygm), which is linked to vision, and vitellogenin (vtg), which is associated with egg provisioning. These genomes set the stage for comparative analyses of genetic structure and selection on the marine organisms that originated with the formation of the CAI.
Archaic Introgression Shapes Genetic Variation at Loci Associated With DNA Virus Load in Modern Humans.
Rajpara R, Polishchuk SS, Yermakovich D … +1 more , Dannemann M
Genome Biol Evol · 2026 May · PMID 42049271 · Full text
Archaic introgression has shaped the modern human immune system, particularly components involved in RNA virus responses. In contrast, its contribution to DNA virus defense remains poorly understood. Here, we investigate...
Archaic introgression has shaped the modern human immune system, particularly components involved in RNA virus responses. In contrast, its contribution to DNA virus defense remains poorly understood. Here, we investigate the contribution of Neandertal- and Denisovan-introgressed haplotypes to viral load of five common DNA viruses in UK Biobank samples, using genome-wide association summary statistics. We identified 18 genome-wide significant associations, predominantly involving Epstein-Barr virus (EBV) and loci within the Major Histocompatibility Complex, including a Denisovan-like haplotype tightly linked to HLA-A*11:01. Notably, the archaic alleles of these haplotypes showed a directional bias toward increased viral loads. Focusing on two chromosome 17 haplotypes associated with higher EBV load, we identified phenotypic associations with blood cell traits and disease markers, as well as functional effects on immune-relevant genes, including GSDMB, ARRB2, and ALOX15. Allele frequency analysis of one of the chromosome 17 haplotypes revealed signatures of shifting modes of selection, possibly reflecting changes in pathogen landscapes over time. Our results suggest that archaic DNA systematically contributes to DNA virus immunity in modern humans, with effects distinct from previously described RNA virus associations. These findings provide novel evolutionary and functional insights into host-virus interactions and the role of archaic admixture in antiviral defense.
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