Reverse engineering high-level resistance to Bt Cry1Ac toxin in Plutella xylostella reveals a hormonal regulatory feedback pathway

Decoding the molecular mechanisms of insect resistance to Bacillus thuringiensis (Bt) toxins is crucial for the sustainable utilization of Bt-based bioinsecticides and transgenic crops. Our previous studies showed that a hormone-responsive transcription factor FOXO binds to an inserted short interspersed nuclear element (SINE, named SE2), causing MAP4K4 overexpression and resistance to Bt Cry1Ac toxin in Plutella xylostella. Furthermore, titers of two upstream signaling hormones (20-hydroxyecdysone and juvenile hormone) were also found to be elevated in the resistant strain, but it was unclear whether this was due to natural variation or a feedback pathway. Here, we established a homozygous knock-in strain (SE2-KI) using a reverse genetic approach to insert the SE2 retrotransposon into the MAP4K4 promoter of a Cry1Ac-susceptible strain. The SE2 insertion induced MAP4K4 overexpression, which in turn caused a downregulation of midgut receptors and an identical resistance phenotype to that seen in the evolved resistant strain. Moreover, SE2 insertion significantly increased the levels of two insect hormones providing definitive evidence for a positive feedback regulatory pathway. This study unveils an as yet uncharacterized hormonal regulatory feedback pathway orchestrating Cry1Ac resistance in P. xylostella, providing new insights into the molecular basis of Bt resistance and informing suitable field resistance management strategies.

Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation

Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1 %. By contrast, ARG levels surged by 17.3 % and 10.9 % on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8 % reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63 % of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.

The Demographic History of Populations and Genomic Imprinting have Shaped the Transposon Patterns in Arabidopsis lyrata

Purifying selection is expected to prevent the accumulation of transposable elements (TEs) within their host, especially when located in and around genes and if affected by epigenetic silencing. However, positive selection may favor the spread of TEs, causing genomic imprinting under parental conflict, as genomic imprinting allows parent-specific influence over resource accumulation to the progeny. Concomitantly, the number and frequency of TE insertions in natural populations are conditioned by demographic events. In this study, we aimed to test how demography and selective forces interact to affect the accumulation of TEs around genes, depending on their epigenetic silencing, with a particular focus on imprinted genes. To this aim, we compared the frequency and distribution of TEs in Arabidopsis lyrata from Europe and North America. Generally, we found that TE insertions showed a lower frequency when they were inserted in or near genes, especially TEs targeted by epigenetic silencing, suggesting purifying selection at work. We also found that many TEs were lost or got fixed in North American populations during the colonization and the postglacial range expansion from refugia of the species in North America, as well as during the transition to selfing, suggesting a potential "TE load." Finally, we found that silenced TEs increased in frequency and even tended to reach fixation when they were linked to imprinted genes. We conclude that in A. lyrata, genomic imprinting has spread in natural populations through demographic events and positive selection acting on silenced TEs, potentially under a parental conflict scenario.

Adaptation repeatedly uses complex structural genomic variation

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation.

Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Transposon is the main component of the eukaryotic genome, and more and more plant genome data show that transposons are diverse in regulating genome structure, variation, function and evolution, with different transposition mechanisms in the genome. Hybridization and polyploidy play an important role in promoting plant speciation and evolution, and recent studies have shown that polyploidy is usually accompanied by the expansion of transposons, which affect the genome size and structure of polyploid plants. Transposons can insert into genes and intergenic regions, resulting in great differences in the overall genome structure of closely related plant species, and it can also capture gene segments in the genome to increase the copy number of genes. In addition, transposons influence the epigenetic modification state of the genome and regulate the expression of the gene, while plant phenotype, biological and abiotic stress response are also regulated by transposons. Overall, transposons play an important role in the plant genome, especially polyploid plant genome, adaptation and evolution.

FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome

BACKGROUND

A nearly complete genome assembly consisting of 14 scaffolds, a total length of 969.6 Mb, and an N50 scaffold length of 99.88 Mb, was generated to better understand how transposable element activity has led to adaptive evolution in Bassia scoparia (kochia), an agronomically important weed.

RESULTS

The nine largest scaffolds correspond to the nine chromosomes of the close relative, Beta vulgaris. From this assembly, 54 387 protein-coding gene loci were annotated. We determined that genes containing Far-Red Elongated Hypocotyl 3 (FHY3) or Far-Red Impaired Response 1 (FAR1) functional domains have undergone a large, kochia-specific gene family expansion. We discovered that putative Mutator Don-Robertson (MuDR) transposable elements with detectable FHY3/FAR1 domains were tightly associated with segmental duplications of 5-enolpyruvylshikimate-3-phosphate synthase subsequently conferring resistance to the herbicide glyphosate. Further, we characterized a new MuDR subtype, named here as 'Muntjac', which contributes to the evolution of herbicide resistance in kochia through the process of transduplication.

CONCLUSION

Collectively, our study provides insights into the role FHY3/FAR1 genes as active transposable elements and contributes new perspectives on the interaction between transposons and herbicide resistance evolution. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake

Of all mutational mechanisms contributing to phenotypic variation, structural variants are both among the most capable of causing major effects as well as the most technically challenging to identify. Intraspecific variation in snake venoms is widely reported, and one of the most dramatic patterns described is the parallel evolution of streamlined neurotoxic rattlesnake venoms from hemorrhagic ancestors by means of deletion of snake venom metalloproteinase (SVMP) toxins and recruitment of neurotoxic dimeric phospholipase A2 (PLA2) toxins. While generating a haplotype-resolved, chromosome-level genome assembly for the eastern diamondback rattlesnake (Crotalus adamanteus), we discovered that our genome animal was heterozygous for a ∼225 Kb deletion containing six SVMP genes, paralleling one of the two steps involved in the origin of neurotoxic rattlesnake venoms. Range-wide population-genomic analysis revealed that, although this deletion is rare overall, it is the dominant homozygous genotype near the northwestern periphery of the species' range, where this species is vulnerable to extirpation. Although major SVMP deletions have been described in at least five other rattlesnake species, C. adamanteus is unique in not additionally gaining neurotoxic PLA2s. Previous work established a superficially complementary north-south gradient in myotoxin (MYO) expression based on copy number variation with high expression in the north and low in the south, yet we found that the SVMP and MYO genotypes vary independently, giving rise to an array of diverse, novel venom phenotypes across the range. Structural variation, therefore, forms the basis for the major axes of geographic venom variation for C. adamanteus.

Transposition of the heat-activated retrotransposon ONSEN results in enhanced hypocotyl elongation

We aimed to identify new mutants resulting from ONSEN transposition in Arabidopsis thaliana by subjecting nrpd1 mutant seedlings to heat stress. We isolated a mutant with a significantly elongated hypocotyl, named Long hypocotyl in ONSEN-inserted line 1 (hyo1). This phenotype was heritable, with progeny consistently displaying longer hypocotyls than the wild type. Genetic analysis revealed that this trait was due to a single recessive mutation. Further mapping and sequencing identified the insertion of ONSEN into the HY2 gene, a crucial regulator of hypocotyl elongation. The insertion disrupted HY2 transcription, as confirmed by quantitative PCR, leading to the observed phenotype. To assess any influence of the nrpd1 background, we generated lines backcrossed twice to wild-type Col-0, and the results were consistent with those observed in the original mutant lines. Furthermore, we examined the effect of HY2 and HYO1 mutations on flowering time by analyzing the expression levels of FT. The hyo1 mutant exhibited earlier flowering compared to both wild type and the nrpd1 mutant, with increased FT expression levels. This research highlights the impact of ONSEN transposition on gene function and phenotypic variation in A. thaliana, providing new insights into the mutagenic potential of transposons and their role in shaping plant traits.

Transposable Element Landscape in the Monotypic Species Barthea barthei (Hance) Krass (Melastomataceae) and Its Role in Ecological Adaptation

Transposable elements (TEs) are crucial for genome evolution and ecological adaptation, but their dynamics in non-model plants are poorly understood. Using genomic, transcriptomic, and population genomic approaches, we analyzed the TE landscape of Barthea barthei (Melastomataceae), a species distributed across tropical and subtropical southern China. We identified 64,866 TE copies (16.76% of a 235 Mb genome), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). A genome-wide analysis revealed 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response. We identified 3859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress response, and secondary metabolism. A transcriptome analysis of the flower buds identified 343 differentially expressed TEs between the ecotypes, 30 of which were near or within differentially expressed genes. The non-random distribution (primarily within 5 kb of genes) and association with adaptive traits suggest a significant role in B. barthei's successful colonization of diverse habitats. Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forests, particularly through their influence on regulatory networks governing stress response and development.

On the origin of the P-element invasion in Drosophila simulans

The horizontal transfer (HT) of the P-element is one of the best documented cases of the HT of a transposable element. The P-element invaded natural D. melanogaster populations between 1950 and 1980 following its HT from Drosophila willistoni, a species endemic to South and Central America. Subsequently, it spread in D. simulans populations between 2006 and 2014, following a HT from D. melanogaster. The geographic region where the spread into D. simulans occurred is unclear, as both involved species are cosmopolitan. The P-element differs between these two species by a single base substitution at site 2040, where D. melanogaster carries a 'G' and D. simulans carries an 'A'. It has been hypothesized that this base substitution was a necessary adaptation that enabled the spread of the P-element in D. simulans, potentially explaining the 30-50-year lag between the invasions of D. melanogaster and D. simulans. To test this hypothesis, we monitored the invasion dynamics of P-elements with both alleles in experimental populations of D. melanogaster and D. simulans. Our results indicate that the allele at site 2040 has a minimal impact on the invasion dynamics of the P-element and, therefore, was not necessary for the invasion of D. simulans. However, we found that the host species significantly influenced the invasion dynamics, with higher P-element copy numbers accumulating in D. melanogaster than in D. simulans. Finally, based on SNPs segregating in natural D. melanogaster populations, we suggest that the horizontal transfer of the P-element from D. melanogaster to D. simulans likely occurred around Tasmania.

Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping

Transposable elements (TEs) are parasitic genomic elements that are ubiquitous across the tree of life and play a crucial role in genome evolution. Advances in long-read sequencing have allowed highly accurate TE detection, though at a higher cost than short-read sequencing. Recent studies using long reads have shown that existing short-read TE detection methods perform inadequately when applied to real data. In this study, we use a machine learning approach (called TEforest) to discover and genotype TE insertions and deletions with short-read data by using TEs detected from long-read genome assemblies as training data. Our method first uses a highly sensitive algorithm to discover potential TE insertion or deletion sites in the genome, extracting relevant features from short-read alignments. To discriminate between true and false TE insertions, we train a random forest model with a labeled ground-truth dataset for which we have calculated the same set of short-read features. We conduct a comprehensive benchmark of TEforest and traditional TE detection methods using real data, finding that TEforest identifies more true positives and fewer false positives across datasets with different read lengths and coverages, while also accurately inferring genotypes and the precise breakpoints of insertions. By learning short-read signatures of TEs previously only discoverable using long reads, our approach bridges the gap between large-scale population genetic studies and the accuracy of long-read assemblies. This work provides a user-friendly tool to study the prevalence and phenotypic effects of TE insertions across the genome.

Transcriptional dynamics and tissue-specific expression patterns of transposable elements in orthopteran insects

Transposable elements (TEs) are prevalent in the genomes of orthopteran insects, contributing significantly to their genome evolution and diversity. In light of the existing gap in our understanding of TEs transcript dynamics in orthopteran insects, we recognize the critical need to undertake comprehensive analyses in this area. Therefore, we have decided to delve into the characterization of TE transcripts, their abundance profiles, and the formation of chimeric transcripts using RNA-seq data and genome assemblies. The transcript analysis of TEs across various species revealed significant differences in TE abundance and expression patterns. In particular, Schistocerca americana exhibited twice the number of transcripts within the genus Schistocerca compared to the average of other species, while Gryllus bimaculatus displayed the lowest number of transcripts. Despite this, all Schistocerca species shared similar fractions of TE transcripts at the clade level, with DNA transposons (45%) being the most abundant, followed by LINE (19%) and LTR elements (18%). Interestingly, Acrida cinerea displayed different TE abundance patterns compared to Schistocerca species, particularly with an increased proportion of LTR transcripts, accounting for 31% of the total transcripts. Further analysis revealed tissue-specific transcriptional activity of TE clades, with notable differences between male and female specimens. In Gryllus bimaculatus, TEs were highly transcribed across ovaries and gut tissues in females compared to male testes and gut. Conversely, Gastrimargus marmoratus displayed higher TE transcription in male tissues compared to females, indicating species-specific expression patterns. A similar pattern has been observed in Acrida cinerea, except in female gonads, where 4618 TEs were transcribed compared to 3757 in male gonads. Despite these variations, no correlation was found between genome size and TE transcript abundance. Additionally, highly conserved TEs were involved in the formation of chimeric transcripts, indicating potential regulatory roles in gene expression. The expression quantification analysis of chimeric TEs and genes revealed tissue-specific expression patterns, and TEs do not control the overall expression of all genes except some, suggesting regulatory roles of TEs in gene expression. Overall, our study underscores tissue-specific variations in TE expression and transcript abundance among different species. Additionally, our findings suggest the involvement of highly conserved TEs in the formation of chimeric transcripts across different species.

An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen

Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.

Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment

Introduction

Rice samples exposed to the space environment have generated diverse phenotypic variations. Miniature-inverted-repeat transposable elements (MITEs), often found adjacent to genes, play a significant role in regulating the plant genome. Herein, the contribution of MITEs in regulating space-mutagenic phenotypes was explored.

Methods

The space-mutagenic phenotype changes in the F3 to F5 generations of three space-mutagenic lines from the rice varieties Dongnong423 (DN423) and Dongnong (DN416) were meticulously traced. Rice leaves samples at the heading stage from three space-mutagenic lines were subjected to high coverage whole-genome bisulfite sequencing and whole-genome sequencing. These analyses were conducted to investigate the effects of MITEs related epigenetic and genetic variations on space-mutagenic phenotypes.

Results and discussion

Studies have indicated that MITEs within gene regulatory regions might contribute to the formation and differentiation of space-mutagenic phenotypes. The space environment has been shown to induce the transposable elements insertion polymorphisms of MITEs (MITEs-TIPs), with a notable preference for insertion near genes involved in stress response and phenotype regulation. The space-induced MITEs-TIPs contributed to the formation of space-mutagenic phenotype by modulating the expression of gene near the insertion site. This study underscored the pivotal role of MITEs in modulating plant phenotypic variation induced by the space environment, as well as the transgenerational stability of these phenotypic variants.

Transcriptional profiles of Microcystis reveal gene expression shifts that promote bloom persistence in in situ mesocosms

Harmful algal blooms caused by cyanobacteria threaten aquatic ecosystems, the economy, and human health. Previous work has tried to identify the mechanisms that allow blooms to form, focusing on the role of nutrients. However, little is known about how introduced nutrients influence gene expression in situ. To address this knowledge gap, we used in situ mesocosms initiated with water experiencing a Microcystis bloom. We added pulses of nutrients that are commonly associated with anthropogenic sources to the mesocosms for 72 hours and collected samples for metatranscriptomics to examine how the physiological function of Microcystis and bloom status changed. The addition of nitrogen (N) as urea, but not the addition of PO4, resulted in conspicuous bloom persistence for at least 9 days after the final introduction of nutrients. The addition of urea initially resulted in the upregulation of photosynthesis machinery, as well as phosphate, carbon, and N transport and metabolism. Once Microcystis presumably became N-replete, upregulation of amino acid metabolism, microcystin biosynthesis, and other processes associated with biomass generation occurred. These capacities coincided with the upregulation of toxin-antitoxin systems, CRISPR-cas genes, and transposases suggesting that phage defense and genome rearrangement are critical in bloom persistence. Overall, our results show the stepwise transcriptional response of a Microcystis bloom to the introduction of nutrients, specifically urea, as it is sustained in a natural setting. The transcriptomic shifts observed herein may serve as markers of the longevity of blooms while providing insight into why Microcystis blooms over other cyanobacteria.IMPORTANCEHarmful algal blooms represent a threat to human health and ecosystems. Understanding why blooms persist may help us develop warning indicators of bloom persistence and create novel mitigation strategies. Using mesocosm experiments initiated with water with an active bloom, we measured the stepwise transcription changes of the toxin-producing cyanobacterium Microcystis in response to the addition of nutrients that are important in causing blooms. We found that nitrogen (N), but not phosphorus, promoted bloom longevity. The initial introduction of N resulted in the upregulation of genes involved in photosynthesis and N import. At later times in the bloom, upregulation of genes involved in biomass generation, phage protection, genomic rearrangement, and toxin production was observed. Our results suggest that Microcystis first fulfills nutritional requirements before investing energy in pathways associated with growth and protection against competitors, which allowed bloom persistence more than a week after the final addition of nutrients.

Population Genomics of Adaptive Radiation

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re-use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization-and the hypothesized processes by which it shapes diversification-and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life.

Comparative analysis of amphibian genomes: An emerging resource for basic and applied research

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long-read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes and lack of high-quality assemblies in multiple clades of amphibians. Here, we analyse 51 publicly available amphibian genomes to evaluate their usefulness for functional genomics research. We report considerable variation in genome assembly quality and completeness and report some of the highest transposable element and repeat contents of any vertebrate. Additionally, we detected an association between transposable element content and climatic variables. Our analysis provides evidence of conserved genome synteny despite the long divergence times of this group, but we also highlight inconsistencies in chromosome naming and orientation across genome assemblies. We discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Finally, we propose increased investment in amphibian genomics research to promote their conservation.

MCHelper automatically curates transposable element libraries across eukaryotic species

The number of species with high-quality genome sequences continues to increase, in part due to the scaling up of multiple large-scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element (TE) sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of TE sequences is still technically challenging. Several de novo TE identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high-quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelper's fully automated mode with the outputs from three de novo TE identification tools, RepeatModeler2, EDTA, and REPET, in the fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the TE libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to ∼48% fewer "unclassified/unknown" TE consensus sequences. Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)

The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress. We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5-Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness. In the long term, 5-Azacytidine treatment alone caused both hypo- and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context-specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level.

Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection

Habitat transitions have shaped the evolutionary trajectory of many clades. Sea catfishes (Ariidae) have repeatedly undergone ecological transitions, including colonizing freshwaters from marine environments, leading to an adaptive radiation in Australia and New Guinea alongside non-radiating freshwater lineages elsewhere. Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species. We investigate how three major ecological transitions have shaped genomic variation among ariids over their ~ 50 million-year evolutionary history. Our results show that relatively younger freshwater lineages exhibit a higher incidence of positive selection than their more ancient marine counterparts. They also display a larger disparity in body shapes, a trend that correlates with a heightened occurrence of positive selection on genes associated with body size and elongation. Although positive selection in the Australia and New Guinea radiation does not stand out compared to non-radiating lineages overall, selection across the prolactin gene family during the marine-to-freshwater transition suggests that strong osmoregulatory adaptations may have facilitated their colonization and radiation. Our findings underscore the significant role of selection in shaping the genome and organismal traits in response to habitat shifts across macroevolutionary scales.

Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates

Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) is present at unusually high levels and its function remains an enigma in dinoflagellates chromosomal DNA for several decades. Here, we demonstrate that 5hmU contents vary among different dinoflagellates and are generated through thymidine hydroxylation. Importantly, we identified the enzyme, which is a putative dinoflagellate TET/JBP homolog, catalyzing 5hmU production using both in vivo and in vitro biochemical assays. Based on the near-chromosomal level genome assembly of dinoflagellate Amphidinium carterae, we depicted a comprehensive 5hmU landscape and found that 5hmU loci are significantly enriched in repeat elements. Moreover, inhibition of 5hmU via dioxygenase inhibitor leads to transcriptional activation of 5hmU-marked transposable elements, implying that 5hmU appears to serve as an epigenetic mark for silencing transposon. Together, our results revealed the biogenesis, genome-wide landscape, and molecular function of dinoflagellate 5hmU, providing mechanistic insight into the function of this enigmatic DNA mark.

Positive selection in cilia-related genes may facilitate deep-sea adaptation of Thermocollonia jamsteci

Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution. In this project, the chromosome-level genome of the deep-sea hydrothermal vent gastropod T. jamsteci was constructed for the first time to examine molecular mechanisms of its adaptation to the deep-sea environment. The genome size was large (2.54 Gb), ranking at the top of all species in the Vetigastropoda subclass, driven primarily by the bursts of transposable elements (TEs). The transposition of TEs may also trigger chromosomal changes including both inter-chromosomal fusions and intra-chromosomal activities involving chromosome inversions, rearrangements and fusions, as revealed by comparing the genomes of T. jamsteci and its closely related shallow-sea species Gibbula magus. Innovative changes including the expansion of the ABC transporter gene family that may facilitate detoxification, duplication of genes related to endocytosis, immunity, apoptosis, and anti-apoptotic domains that may help T. jamsteci fight against microbial pathogens, were identified. Furthermore, comparative analysis identified positive selection signals in a large number of genes including the hypoxia up-regulated protein 1, which is a chaperone that may promote adaptation of the T. jamsteci to hypoxic deepsea environments, hox2, Rx2, Pax6 and cilia-related genes BBS1, BBS2, BBS9 and RFX4. Notably, because of the critical importance of cilia and IFT in development, positive selection in cilia-related genes may play a critical role in facilitating T. jamsteci to adapt to the high-pressure deep-sea ecosystem. Results from this study thus revealed important molecular clues that may facilitate further research on the adaptation of molluscs to deep-sea hydrothermal vents.

Myzus persicae resistance to neonicotinoids-unravelling the contribution of different mechanisms to phenotype

BACKGROUND

Deciphering the mechanisms underlying insecticide resistance is key to devising appropriate strategies against this economically important trait. Myzus persicae, the green peach-potato aphid, is a major pest that has evolved resistance to many insecticide classes, including neonicotinoids. M. persicae resistance to neonicotinoids has previously been shown to result from two main mechanisms: metabolic resistance resulting from P450 overexpression and a targetsite mutation, R81T. However, their respective contribution to resistant phenotypes remains unclear.

RESULTS

By combining extensive insecticide bioassays with and without addition of the synergist PBO, and gene copy number and expression quantification of two key P450 enzymes (CYP6CY3 and CYP6CY4) in a 23 clone collection, we, (i) confirmed that metabolic resistance is correlated with P450 expression level, up to a threshold, (ii) demonstrated that the R81T mutation, in the homozygous state and in combination with P450 overexpression, leads to high levels of resistance to neonicotinoids, and, (iii) showed that there is a synergistic interaction between the P450 and R81T mechanisms, and that this interaction has the strongest impact on the strength of resistance phenotypes. However, even though the R81T mutation has a great effect on the resistance phenotype, different R81T genotypes can exhibit variation in the level of resistance, explained only partially by P450 overexpression.

CONCLUSION

To comprehend resistance phenotypes, it is important to take into account every mechanism at play, as well as the way these mechanisms interact. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide

The mobilization of transposable elements is a potent source of mutations. In plants, several stransposable elements respond to external cues, fuelling the hypothesis that natural transposition can create environmentally sensitive alleles for adaptation. Here we report on the detailed characterization of a retrotransposon insertion within the first intron of the Arabidopsis floral-repressor gene FLOWERING LOCUS C (FLC) and the discovery of its role for adaptation. The insertion mutation augments the environmental sensitivity of FLC by affecting the balance between coding and non-coding transcripts in response to stress, thus expediting flowering. This balance is modulated by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatic sequences. The stress-sensitive allele of FLC has spread across populations subjected to recurrent chemical weeding, and we show that retrotransposon-driven acceleration of the life cycle represents a rapid response to herbicide application. Our work provides a compelling example of a transposable element-driven environmentally sensitive allele that confers an adaptive response in nature.

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei

The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa in 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of the CBB, with 93% of the genome assembled into 14 scaffolds. Whole genome sequencing of pooled samples from different populations across Jamaica showed that the CBB harbors low levels of genetic diversity alongside an excess of low-frequency alleles, indicative of a recent genetic bottleneck. The analyses also showed a recent surge in the activity of transposable elements (TEs), particularly LINE/R1 and LTR/Gypsy elements, within CBB populations. Our findings offer first insights into the evolutionary genomics of CBB populations in Jamaica, highlighting the potential role of TEs in shaping the genome of this important pest species.

Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis

Multiple sclerosis (MS) is an autoimmune-demyelinating disease with an inflammatory pathology formed by self-reactive lymphocytes with activated glial cells. Progressive MS, characterized by resistance to medications, significantly differs from the non-progressive form in gut microbiome profiles. After confirming an increased abundance of "Tyzzerella nexilis" in various cohorts of progressive MS, we identified a distinct cluster of T. nexilis strains enriched in progressive MS based on long-read metagenomics. The distinct T. nexilis cluster is characterized by a large number of mobile genetic elements (MGEs) and a lack of defense systems against MGEs. Microbial genes for sulfate reduction and flagella formation with pathogenic implications are specific to this cluster. Moreover, these flagellar genes are encoded on MGEs. Mono-colonization with MGE-enriched T. nexilis made germ-free mice more susceptible to experimental autoimmune encephalomyelitis. These results indicate that the progression of MS may be promoted by MGE-enriched T. nexilis with potentially pathogenic properties.

Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype

The Microcystis mobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain, Microcystis aeruginosa PCC 7086, and a non-toxigenic genetic mutant, Microcystis aeruginosa PCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyB strain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyB isolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights how Microcystis strains continue to "evolve" in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences between Microcystis strains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments.

Agricultural insect pests as models for studying stress-induced evolutionary processes

Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.

Transposable elements in Drosophila montana from harsh cold environments

BACKGROUND

Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates.

RESULTS

Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints.

CONCLUSIONS

Our research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.

Metagenomics of high-altitude groundwater reveal different health risks associated with antibiotic-resistant pathogens and bacterial resistome in the latitudinal gradient

Groundwater on the Tibetan Plateau is a critical water resource to people in Asia. However, its prevalence of antibiotic-resistant pathogens (ARPs), bacterial resistome and their driving factors remain unknown. Using metagenomics analysis, a hotspot of antibiotic-resistance genes (ARGs) and last-resort ARGs (LARGs) with a total of 639 subtypes was identified in the groundwater. Importantly, 164 metagenome-assembled genomes (MAGs) which possessed both ARGs and virulence factors (VFs) were assigned as potential ARPs, with the most abundant species being Acinetobacter johnsonii and Acinetobacter pittii. A total of 157 potential ARPs, involving Escherichia coli, were predicted as "natural" ARGs supercarriers. Thirty-six ARPs dominated by the genus Acinetobacter and Pseudomonas were found to harbour LARGs. Co-localizations of the ARG-mobile genetic elements (MGEs) showed that MGEs were significantly associated with ARGs in the ARPs, which suggests ARPs play a prominent role in ARG dissemination. Notably, latitudinal gradient is a driving factor in the occurrence of ARGs and ARPs. The average abundances of ARGs and ARP decreased as the latitude increased, with the highest abundance occurring in the region between 28.6◦N and 29.5◦N. MetaCompare further revealed health risks associated with the resistome decreased as the latitudes increased. These findings indicated different health risks associated with ARPs and bacterial resistome in latitudinal gradient groundwater. They raise the concerns of mitigating ARPs risk in groundwater on the Tibetan Plateau.

Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila

A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana

Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 h post inoculation [hpi]) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi. These DEGs were predominantly associated with defense response, ethylene, and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly upregulated after inoculation, and more of them were enriched near genes in Colfax than other soybean lines. Notably, we identified a long non-coding RNA (lncRNA) within the mapped region of the resistance gene that exhibited exclusive upregulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH (where H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

Genomics resources for the Rapa Nui (Eastern Island) spiny lobster Panulirus pascuensis (Crustacea: Decapoda: Achelata)

Background

The Easter Island spiny lobster Panulirus pascuensis (Reed, 1954) or ‘Ura’ in the Rapa Nui language, is a little known species native to the south eastern Pacific Ocean, distributed along the coasts of Easter Island, Pitcairn Island, and the Salas y Gómez Ridge. In Easter Island, P. pascuensis is the target of a small and profitable and probably overexploited fishery. In this study, we profited from a series of bioinformatic analyses to mine biological insight from low-pass short-read next generation sequencing datasets; we have estimated genome size and ploidy in P. pascuensis using a k-mer strategy, discovered, annotated, and quantified mobile elements in the nuclear genome, assembled the 45S rRNA nuclear DNA cassette and mitochondrial chromosome, and explored the phylogenetic position of P. pascuensis within the genus Panulirus using the signal retrieved from translated mitochondrial protein coding genes.

Results

K-mer analyses predicted P. pascuensis to be diploid with a haploid genome size ranging between 2.75 Gbp (with k-mer = 51) and 3.39 Gbp (with k-mer = 18). In P. pascuensis, repetitive elements comprise at least a half and a maximum of three fourths of the nuclear genome. Almost a third (64.94%) of the repetitive elements present in the studied nuclear genome were not assigned to any known family of transposable elements. Taking into consideration only annotated repetitive elements, the most abundant were classified as Long Interspersed Nuclear Elements (22.81%). Less common repetitive elements included Long Terminal Repeats (2.88%), Satellite DNA (2.66%), and DNA transposons (2.45%), among a few others. The 45S rRNA DNA cassette of P. pascuensis was partially assembled into two contigs. One contig, 2,226 bp long, encoded a partially assembled 5′ ETS the entire ssrDNA (1,861 bp), and a partial ITS1. A second contig, 6,714 bp long, encoded a partially assembled ITS1, the entire 5.8S rDNA (158 bp), the entire ITS2, the entire lsrDNA (4,938 bp), and a partial 3′ ETS (549 bp). The mitochondrial genome of P. pascuensis was 15,613 bp long and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes (12S ribosomal RNA [rrnS] and 16S ribosomal RNA [rrnL]). A phylomitogenomic analysis based on PCGs retrieved Panulirus pascuensis as sister to a fully supported clade comprising P. cygnus and P. longipes.

Conclusion

We expect that the information generated in this study will guide the assembly of a chromosome-level nuclear genome for P. pascuensis in the near future. The newly assembled 45S rRNA nuclear DNA cassette and mitochondrial chromosome can support bioprospecting and biomonitoring of P. pascuensis using environmental DNA. The same elements can help to survey the public market place and detect mislabelling of this and other spiny lobsters. Overall, the genomic resources generated in this study will aid in supporting fisheries management and conservation strategies in this iconic spiny lobster that is likely experiencing overexploitation.

Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus

The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.

Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective

Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.

Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation

Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.

Assessing genotoxic effects of plastic leachates in Drosophila melanogaster

Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of concern given the wide amount of plastic waste, particularly in terrestrial environments, where soil represents a sink for these novel contaminants and a possible pathway of human health risk. In this study, we integrated genetic, molecular, and behavioral approaches to comparatively evaluate toxicological effects of plastic leachates, virgin and oxodegradable polypropylene (PP) and polyethylene (PE), in Drosophila melanogaster, a novel in vivo model organism for environmental monitoring studies and (eco)toxicological research. The results of this study revealed that while conventional toxicological endpoints such as developmental times and longevity remain largely unaffected, exposure to plastic leachates induces chromosomal abnormalities and transposable element (TE) activation in neural tissues. The combined effects of DNA damage and TE mobilization contribute to genome instability and increase the likelihood of LOH events, thus potentiating tumor growth and metastatic behavior ofRasV12 clones. Collectively, these findings indicate that plastic leachates exert genotoxic effects in Drosophila thus highlighting potential risks associated with leachate-related plastic pollution and their implications for ecosystems and human health.

Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

Genetic response of a perennial grass to warm and wet environments interacts and is associated with trait means as well as plasticity

The potential for rapid evolution is an important mechanism allowing species to adapt to changing climatic conditions. Although such potential has been largely studied in various short-lived organisms, to what extent we can observe similar patterns in long-lived plant species, which often dominate natural systems, is largely unexplored. We explored the potential for rapid evolution in Festuca rubra, a long-lived grass with extensive clonal growth dominating in alpine grasslands. We used a field sowing experiment simulating expected climate change in our model region. Specifically, we exposed seeds from five independent seed sources to novel climatic conditions by shifting them along a natural climatic grid and explored the genetic profiles of established seedlings after 3 years. Data on genetic profiles of plants selected under different novel conditions indicate that different climate shifts select significantly different pools of genotypes from common seed pools. Increasing soil moisture was more important than increasing temperature or the interaction of the two climatic factors in selecting pressure. This can indicate negative genetic interaction in response to the combined effects or that the effects of different climates are interactive rather than additive. The selected alleles were found in genomic regions, likely affecting the function of specific genes or their expression. Many of these were also linked to morphological traits (mainly to trait plasticity), suggesting these changes may have a consequence on plant performance. Overall, these data indicate that even long-lived plant species may experience strong selection by climate, and their populations thus have the potential to rapidly adapt to these novel conditions.

Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.

Mapping and functional characterization of structural variation in 1060 pig genomes

BACKGROUND

Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.

RESULTS

We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies.

CONCLUSIONS

This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Effects of Arboviral Infections on Transposable Element Transcript Levels in Aedes aegypti

Transposable elements are mobile repeated sequences found in all genomes. Transposable elements are controlled by RNA interference pathways in most organisms, and this control involves the PIWI-interacting RNA pathway and the small interfering RNA pathway, which is also known to be the first line of antiviral defense in invertebrates. Using Drosophila, we recently showed that viral infections result in the modulation of transposable element transcript levels through modulation of the small RNA repertoire. The Aedes aegypti mosquito is of particular interest because almost half of its genome is made of transposable elements, and it is described as a major vector of viruses (such as the dengue [DENV], Zika [ZIKV], and chikungunya [CHIKV] arboviruses). Moreover, Aedes mosquitoes are unique among insects in that the PIWI-interacting RNA pathway is also involved in the somatic antiviral response, in addition to the transposable element control and PIWI-interacting RNA pathway genes expanded in the mosquito genome. For these reasons, we studied the impacts of viral infections on transposable element transcript levels in A. aegypti samples. We retrieved public datasets corresponding to RNA-seq data obtained from viral infections by DENV, ZIKV, and CHIKV in various tissues. We found that transposable element transcripts are moderately modulated following viral infection and that the direction of the modulation varies greatly across tissues and viruses. These results highlight the need for an in-depth investigation of the tightly intertwined interactions between transposable elements and viruses.

The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role

Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century

Transposable element invasions have a profound impact on the evolution of genomes and phenotypes. It is thus an important open question how often such TE invasions occur. To address this question, we utilize the genomes of historical specimens, sampled about 200 y ago. We found that the LTR retrotransposons Blood, Opus, and 412 spread in Drosophila melanogaster in the 19th century. These invasions constitute second waves, as degraded fragments were found for all three TEs. The composition of Opus and 412, but not of Blood, shows a pronounced geographic heterogeneity, likely due to founder effects during the invasions. Finally, we identified species from the Drosophila simulans complex as the likely origin of the TEs. We show that in total, seven TE families invaded D. melanogaster during the last 200y, thereby increasing the genome size by up to 1.2Mbp. We suggest that this high rate of TE invasions was likely triggered by human activity. Based on the analysis of strains and specimens sampled at different times, we provide a detailed timeline of TE invasions, making D. melanogaster the first organism where the invasion history of TEs during the last two centuries could be inferred.

The global distribution of angiosperm genome size is shaped by climate

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis

Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.

Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle

Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.

Plant adaptation to ionizing radiation: Mechanisms and patterns

Adaptation to environmental stressors is an essential property of plants that allows them, despite an immobile lifestyle, to survive in a changeable environment. The chain of successive events culminating in the final radiobiological reaction begins with the absorption of energy of ionizing radiation in the cell. Starting from stochastic acts of molecular injury formation, radiation damage gradually acquires deterministic features, which are expressed in a limited number of phenomena that complete plant radiation damage. As plants undergo specialization, the differences between plants and animals become more pronounced, leading to distinct responses to radiation. Chronic radiation exposure may activate biological mechanisms resulting in increased radioresistance of the population. The higher the level of radiation exposure and the sensitivity of plants to radiation, the more intensive the selection. Depending on the circumstances, enhanced radioresistance of a population can be achieved in different ways or has not evolved at all. High dose rates of chronic irradiation leаd to selection for the efficiency of repair systems, while low dose rates activate epigenetic mechanisms that lead to the maintenance of oxidative balance, additional synthesis of chaperones, and control of TEs transposition. Due to huge differences in the radiosensitivity of organisms that make up the ecosystem, irradiation can result in disruption of connections between components of ecosystems which may lead to consequences that can differ drastically from those expected at the organismal and population levels. Therefore, the use of ecological knowledge is essential for understanding the responses of populations and ecosystems to radiation exposure.