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Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Transposable elements (TEs) drive genome evolution and can affect gene expression through diverse mechanisms. In breast cancer, disrupted regulation of TE sequences may facilitate tumor-specific transcriptomic alterations. We examine 142,514 full-length isoforms derived from long-read RNA sequencing (LR-seq) of 30 breast samples to investigate the effects of TEs on the breast cancer transcriptome. Approximately half of these isoforms contain TE sequences, and these contribute to half of the novel annotated splice junctions. We quantify splicing of these LR-seq derived isoforms in 1,135 breast tumors from The Cancer Genome Atlas (TCGA) and 1,329 healthy tissue samples from the Genotype-Tissue Expression (GTEx), and find 300 TE-overlapping tumor-specific splicing events. Some splicing events are enriched in specific breast cancer subtypes – for example, a TE-driven transcription start site upstream of ERBB2 in HER2 + tumors, and several TE-mediated splicing events are associated with patient survival and poor prognosis. The full-length sequences we capture with LR-seq reveal thousands of isoforms with signatures of RNA editing, including a novel isoform belonging to RHOA; a gene previously implicated in tumor progression. We utilize our full-length isoforms to discover polymorphic TE insertions that alter splicing and validate one of these events in breast cancer cell lines. Together, our results demonstrate the widespread effects of dysregulated TEs on breast cancer transcriptomes and highlight the advantages of long-read isoform sequencing for understanding TE biology. TE-derived isoforms may alter the expression of genes important in cancer and can potentially be used as novel, disease-specific therapeutic targets or biomarkers. One sentence summary: Transposable elements generate alternative isoforms and alter post-transcriptional regulation in human breast cancer. [ABSTRACT FROM AUTHOR]

Background: The flea beetle Omophoita octoguttata (Coleoptera, Chrysomelidae) is a member of a group in which the males completely lack meiotic recombination (male-specific achiasmy) and that have extraordinarily large X and Y chromosomes. We combined genome sequencing, including microdissected Y and X chromosomes, and cytogenetic in situ hybridization studies, to evaluate the potential role of satellite DNAs (satDNAs) in the differentiation of those gigantic sex chromosomes. Results: We report flow cytometry results showing that this species has a very large genome size (estimated to be 4.61 and 5.47 pg, or roughly 4.6 and 5.5 gigabases, for males and females, respectively), higher than the estimates from two other Alticinae species without giant sex chromosomes, suggesting that these sequences have greatly expanded on both the sex chromosomes, and that the Y has not greatly shrunk like the ones of other insects such as Drosophila with male achiasmy. About 68% of this large genome is made up of repetitive DNAs. Satellite DNAs (OocSatDNAs) form ~ 8–9% of their genomes, and we estimate how much of the sex chromosome expansions occurred due to differential amplification of different satellite classes. Analysis of divergence between sequences in the X and Y chromosomes suggests that, during the past roughly 20 mya, different OocSatDNAs amplified independently, leading to different representations. Some are specific to the Y or X chromosome, as expected when males are achiasmate, completely preventing genetic exchanges between the Y and X. [ABSTRACT FROM AUTHOR]

Human pluripotent stem cells (hPSCs) exist in multiple, transcriptionally distinct states and serve as powerful models for studying human development. Despite their significance, the molecular determinants and pathways governing these pluripotent states remain incompletely understood. Here, we demonstrate that transposable elements act as sensitive indicators of distinct pluripotent cell states. We engineered hPSCs with fluorescent reporters to capture the temporal expression dynamics of two state-specific transposable elements, LTR5_Hs, and MER51B. This dual reporter system enables real-time monitoring and isolation of stem cells transitioning from naïve to primed pluripotency and further towards differentiation, serving as a more accurate readout of pluripotency states compared to conventional systems. Unexpectedly, we identified a rare, metastable cell population within primed hPSCs, marked by transcripts related to preimplantation embryo development and which is associated with a DNA damage response. Moreover, our system establishes the chromatin factor NSD1 and the RNA-binding protein FUS as potent molecular safeguards of primed pluripotency. Our study introduces a novel system for investigating cellular potency and provides key insights into the regulation of embryonic development. Synopsis: A novel dual reporter system based on transposable elements LTR5_Hs and MER51B enables precise tracking of human pluripotent stem cell states. This system reveals also a rare, metastable primed cell population triggered by DNA damage. Transposable elements (TEs) serve as selective indicators of human pluripotency states. LTR5_Hs and MER51B show dynamic expression patterns during different pluripotency states and stem cell differentiation. Concurrent LTR5_Hs and MER51B expression marks rare, metastable primed cells associated with DNA damage. The dual LTR5_Hs/MER51B reporter system enables the identification of regulators of cell potency. A novel dual reporter system based on transposable elements LTR5_Hs and MER51B enables precise tracking of human pluripotent stem cell states. This system reveals also a rare, metastable primed cell population triggered by DNA damage. [ABSTRACT FROM AUTHOR]

Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements. [ABSTRACT FROM AUTHOR]

Background: Myelodysplastic neoplasms (MDS) are heterogeneous hematopoietic disorders characterized by ineffective hematopoiesis and genome instability. Mobilization of transposable elements (TEs) is an important source of genome instability leading to oncogenesis, whereas small PIWI-interacting RNAs (piRNAs) act as cellular suppressors of TEs. However, the roles of TEs and piRNAs in MDS remain unclear. Methods: In this study, we examined TE and piRNA expression through parallel RNA and small RNA sequencing of CD34+ hematopoietic stem cells from MDS patients. Results: Comparative analysis of TE and piRNA expression between MDS and control samples revealed several significantly dysregulated molecules. However, significant differences were observed between lower-risk MDS (LR-MDS) and higher-risk MDS (HR-MDS) samples. In HR-MDS, we found an inverse correlation between decreased TE levels and increased piRNA expression and these TE and piRNA levels were significantly associated with patient outcomes. Importantly, the upregulation of PIWIL2, which encodes a key factor in the piRNA pathway, independently predicted poor prognosis in MDS patients, underscoring its potential as a valuable disease marker. Furthermore, pathway analysis of RNA sequencing data revealed that dysregulation of the TE‒piRNA axis is linked to the suppression of processes related to energy metabolism, the cell cycle, and the immune response, suggesting that these disruptions significantly affect cellular activity. Conclusions: Our findings demonstrate the parallel dysregulation of TEs and piRNAs in HR-MDS patients, highlighting their potential role in MDS progression and indicating that the PIWIL2 level is a promising molecular marker for prognosis. [ABSTRACT FROM AUTHOR]

Avian genomes exhibit compact organization and remarkable chromosomal stability. However, the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored. This study generated a diploid genome assembly for the golden pheasant (Chrysolophus pictus), a species distinguished by the vibrant plumage of males. Each haploid genome assembly included complete chromosomal models, incorporating all microchromosomes. Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes (dot chromosomes), with an average copy number of 54. Structural variation between the haploid genomes was primarily shaped by large insertions and deletions (indels), with minimal contributions from inversions or duplications. Approximately 28% of these large indels were associated with recent insertions of transposable elements, despite their typically low activity in bird genomes. Evidence for significant effects of transposable elements on gene expression was minimal. Evolutionary strata on the sex chromosomes were identified, along with a drastic rearrangement of the W chromosome. These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes. [ABSTRACT FROM AUTHOR]

The coinciding increase in genomics resources for weedy plant species and herbicide resistance evolution has led to a rapid expansion of our understanding of the relationship between genomic structural variation and herbicide resistance mechanisms. Since the first discovery of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation conferring glyphosate resistance in Amaranthus palmeri, we have seen rapid convergent evolution of the same herbicide-resistance mechanism in eleven diverse weed species by a variety of unique structural variant-generating mechanisms. These mechanisms include extrachromosomal circular DNA replication, unequal crossing over, and subtelomeric duplication. More recently, target-site duplication has been found to cause resistance for other herbicides with different modes of action, including acetyl-CoA carboxylase (ACCase) inhibitors and glutamine synthetase inhibitors. Additionally, the first transposon-generated structural variants that confer herbicide resistances are beginning to be discovered. This review summarizes our current understanding of structural variation in agronomic weed genomes as it relates to herbicide resistance and emphasizes necessary future research to clarify the size, nature, and mechanisms that give rise to genomic structural variation. While we limit our review to herbicide resistance traits, this work also highlights the importance of structural variation as a critical component of total genetic diversity and its importance for the rapid evolution of novel traits. [ABSTRACT FROM AUTHOR]

The conducted GWAS identified the association of osteoarthritis with more than 100 different SNPs, most of which are located in intronic and intergenic regions where genes encoding transposable elements and noncoding RNAs derived from them are located. A number of studies have also determined the activation of retroelements in joint tissues and in peripheral blood of patients with osteoarthritis. An assumption has been made that activated transposons, which cause aging and associated inflammation, influence the etiopathogenesis of osteoarthritis. To confirm this hypothesis, a search was conducted for data on changes in the expression of specific microRNAs derived from transposons during aging and osteoarthritis. As a result, 23 such microRNAs were found, the participation of which in the development of the disease is associated with an impact on genes and signaling pathways regulating cell proliferation and apoptosis, inflammatory and metabolic processes, and mechanisms of cartilage degradation. Changes in expression of these microRNAs indicate that the epigenetic mechanisms of aging are involved in osteoarthritis etiopathogenesis owing to pathological activation of transposable elements complementary to the sequences of noncoding RNAs derived from them in evolution. [ABSTRACT FROM AUTHOR]

Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper, we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions (URs) of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of URs that lack annotations, which we call "anonymous." The longest anonymous UR in the Tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a UR implies that URs might be given priority when annotating mammalian genomes. Our documented pipeline for annotating URs in any mammalian genome is available from the repository github.com/evolbioinf/auger ; the additional data for this study are available from the dataverse at doi.org/10.17617/3.4IKQAG. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) can make up more than 50% of any given vertebrate's genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of the mobilome over macroevolutionary timescales remains unclear. We investigated the degree to which the teleost genome duplication (TGD) shaped the diversification trajectory of the teleost mobilome. We integrate a new high coverage genome of Polypterus bichir with data from over 100 publicly available actinopterygian genomes to assess the macroevolutionary implications of genome duplication events on TE evolution in teleosts. Our results provide no evidence for a substantial shift in mobilome composition following the TGD event. Instead, the diversity of the teleost mobilome appears to have been shaped by a history of lineage-specific shifts in composition that are not correlated with commonly evoked drivers of diversification such as body size, water column usage, or latitude. Collectively, these results provide additional evidence for an emerging perspective that TGD did not catalyze bursts of diversification and innovation in the actinopterygian mobilome. [ABSTRACT FROM AUTHOR]

Background: Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11–17, yet causal variants remain elusive. It is therefore important to define the full spectrum of genetic variants in the wider regions surrounding these significantly associated loci. The hypothesis we evaluate here is that unrecognised or relatively unexplored variants in these regions exist and are promising targets for future functional analyses. To test this hypothesis, we implemented a novel approach with targeted nanopore sequencing (Oxford Nanopore Technologies) for 200 kb regions centred on each of the eight AN-associated loci in 10 AN case samples. Our bioinformatics pipeline entailed base-calling and alignment with Dorado and minimap2 software, followed by variant calling with four separate tools, Sniffles2, Clair3, Straglr, and NanoVar. We then leveraged publicly available databases to characterise these loci in putative functional context and prioritise a subset of potentially relevant variants. Results: Targeted nanopore sequencing effectively enriched the target regions (average coverage 14.64x). To test our hypothesis, we curated a list of 20 prioritised variants in non-coding regions, poorly represented in the current human reference genome but that may have functional consequences in AN pathology. Notably, we identified a polymorphic SINE-VNTR-Alu like sub-family D element (SVA-D), intergenic with IP6K2 and PRKAR2A, and a poly-T short tandem repeat (STR) in the 3ʹUTR of FOXP1. Conclusions: Our results highlight the potential of targeted nanopore sequencing for characterising poorly resolved or complex variation, which may be initially obscured in risk-associated regions detected by GWAS. Some of the variants identified in this way, such as the polymorphic SVA-D and poly-T STR, could contribute to mechanisms of phenotypic risk, through regulation of several neighbouring genes implicated in AN biology, and affect post-transcriptional processing of FOXP1, respectively. This exploratory investigation was not powered to detect functional effects, however, the variants we observed using this method are poorly represented in the current human reference genome and accompanying databases, and further examination of these may provide new opportunities for improved understanding of genetic risk mechanisms of AN. [ABSTRACT FROM AUTHOR]

Background: Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes. LTRs contain regulatory sequences essential for the life cycle of the retrotransposon. Previous experimental and sequence studies have provided only limited information about LTR structure and composition, mostly from model systems. To enhance our understanding of these key sequence modules, we focused on the contrasts between LTRs of various retrotransposon families and other genomic regions. Furthermore, this approach can be utilized for the classification and prediction of LTRs. Results: We used machine learning methods suitable for DNA sequence classification and applied them to a large dataset of plant LTR retrotransposon sequences. We trained three machine learning models using (i) traditional model ensembles (Gradient Boosting), (ii) hybrid convolutional/long and short memory network models, and (iii) a DNA pre-trained transformer-based model using k-mer sequence representation. All three approaches were successful in classifying and isolating LTRs in this data, as well as providing valuable insights into LTR sequence composition. The best classification (expressed as F1 score) achieved for LTR detection was 0.85 using the hybrid network model. The most accurate classification task was superfamily classification (F1=0.89) while the least accurate was family classification (F1=0.74). The trained models were subjected to explainability analysis. Positional analysis identified a mixture of interesting features, many of which had a preferred absolute position within the LTR and/or were biologically relevant, such as a centrally positioned TATA-box regulatory sequence, and TG..CA nucleotide patterns around both LTR edges. Conclusions: Our results show that the models used here recognized biologically relevant motifs, such as core promoter elements in the LTR detection task, and a development and stress-related subclass of transcription factor binding sites in the family classification task. Explainability analysis also highlighted the importance of 5'- and 3'- edges in LTR identity and revealed need to analyze more than just dinucleotides at these ends. Our work shows the applicability of machine learning models to regulatory sequence analysis and classification, and demonstrates the important role of the identified motifs in LTR detection. [ABSTRACT FROM AUTHOR]

Repetitive elements can cause large‐scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain chromosomal rearrangements that lead to karyotype changes such as fusions and fissions. This is because chromosome segregation during cell division should be less affected than in organisms with a localized centromere. The relationships between repetitive elements and chromosomal rearrangements and how they may translate to patterns of speciation in holocentric organisms are though poorly understood. Here, we use a reference‐free approach based on low‐coverage short‐read sequencing data to characterize the repeat landscape of two independently evolved holocentric groups: Erebia butterflies and Carex sedges. We consider both micro‐ and macro‐evolutionary scales to investigate the repeat landscape differentiation between Erebia populations and the association between repeats and karyotype changes in a phylogenetic framework for both Erebia and Carex. At a micro‐evolutionary scale, we found population differentiation in repeat landscape that increases with overall intraspecific genetic differentiation among four Erebia species. At a macro‐evolutionary scale, we found indications for an association between repetitive elements and karyotype changes along both Erebia and Carex phylogenies. Altogether, our results suggest that repetitive elements are associated with the level of population differentiation and chromosomal rearrangements in holocentric clades and therefore likely play a role in adaptation and potentially species diversification. [ABSTRACT FROM AUTHOR]

Zygotic genome activation (ZGA) is critical for early embryo development and is meticulously regulated by epigenetic modifications. H3K4me3 is a transcription-permissive histone mark preferentially found at promoters, but its distribution across genome features remains incompletely understood. In this study, we investigated the genome-wide enrichment of H3K4me3 during early embryo development and embryonic stem cells (ESCs) in both sheep and mice. We discovered that broad H3K4me3 domains were present in MII stage oocytes and were progressively diminished, while promoter H3K4me3 enrichment was increased and correlated with gene upregulation during ZGA in sheep. Additionally, we reported the dynamic distribution of H3K4me3 at the transposable elements (TEs) during early embryo development in both sheep and mice. Specifically, the H3K4me3 distribution of LINE1 and ERVL, two subsets of TEs, was associated with their expression during early embryo development in sheep. Furthermore, H3K4me3 enrichment in TEs was greatly increased during ZGA following Kdm5b knockdown, and the distribution of RNA polymerase II (Pol2) in TEs was also markedly increased in Kdm5b knockout ESCs in mice. These findings suggest that H3K4me3 plays important roles in regulating TE expression through interaction with RNA Pol2, providing valuable insights into the regulation of ZGA initiation and cell fate determination by H3K4me3. [ABSTRACT FROM AUTHOR]

In mammals, fertilization is followed by extensive reprogramming and reorganization of the chromatin accompanying the transcriptional activation of the embryo. This reprogramming results in blastomeres with the ability to give rise to all cell types and a complete organism, including extra‐embryonic tissues, and is known as totipotency. Transcriptional activation occurs in a process known as zygotic genome activation (ZGA) and is tightly linked to the expression of transposable elements, including endogenous retroviruses (ERVs) such as endogenous retrovirus with leucine tRNA primer (ERVL). Recent studies discovered the importance of ERVs in this process, yet the race to decipher the network surrounding these elements is still ongoing, and the molecular mechanism behind their involvement remains a mystery. Amid a recent surge of studies reporting the discovery of various factors and pathways involved in the regulation of ERVs, this review provides an overview of the knowns and unknowns in the field, with a particular emphasis on the chromatin landscape and how ERVs shape preimplantation development in mammals. In so doing, we highlight recent discoveries that have advanced our understanding of how these elements are involved in transforming the quiescent zygote into the most powerful cell type in mammals. [ABSTRACT FROM AUTHOR]

Summary: Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high‐quality near telomere‐to‐telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present‐day U‐genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub‐populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat. [ABSTRACT FROM AUTHOR]

Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) play a crucial role in placental development and dysfunction. Our study examined TE expression in pre-eclampsia (PE) using RNA-seq datasets. We identified differentially expressed TEs and explored the genomic location of the most significant TEs, investigating their possible regulatory roles. Notably, three TEs overlapped with putative enhancer regions, suggesting a potential regulatory impact on gene expression. These findings highlight the regulatory potential of TEs and their importance in placental development, supporting that TE dysregulation may contribute to PE pathogenesis. • Transposable element dysregulation is a feature of pre-eclampsia. • Upregulated transposable elements in pre-eclampsia show overlap with enhancers. • Transposable element upregulation in pre-eclampsia suggests regulatory roles. • Dysregulated transposable elements reveal potential diagnostic/therapeutic targets. [ABSTRACT FROM AUTHOR]

Insertions of the transposable element IS5 into its target sites in response to stressful environmental conditions, DNA structures, and DNA-binding proteins are well studied, but how the genomic contexts near IS5′s native loci impact its transpositions is largely unknown. Here, by examining the roles of all 11 copies of IS5 within the genome of E. coli strain BW25113 in transposition, we reveal that the most significant copy of IS5 is one nested within and oriented in the same direction as the nmpC gene, while two other copies of IS5 harboring point mutations are hardly transposed. Transposition activity is heavily reliant on the upstream nmpC promoter that drives IS5 transposase gene ins5A, with more transpositions resulting from greater promoter activity. The IS5 element at nmpC but not at other loci transcribed detectable amounts of ins5A mRNA. By increasing expression of the ins5CB operon harbored in IS5, we demonstrate that Ins5B and Ins5C appear to exert a stimulatory role in IS5 transposition, suggesting that the downstream genomic regions near the native loci are involved in overall IS5 transposition as well. Using a strain that carries IS5 only at the nmpC locus, we confirm that IS5 primarily uses a copy/paste mechanism for transposition, although we cannot rule out the cut/paste mechanism. [ABSTRACT FROM AUTHOR]

The genetic basis of phenotypes in Drosophila, is often difficult to explain via genetic mapping approaches. Likewise, phenotypic differences between male and female of the same species (i. e. sexual dimorphism) cannot be fully explained by gene expression differences between two sexes, since number of differentially expressed genes is very high for complex sex specific phenotype. Recent advances in DNA sequencing technologies have demonstrated that transposable elements (TEs) are widespread in all genomes, representing a substantial part of the genome. However, the role of TEs in genome regulation and maintenance of genome size phenotype of a species is not clearly understood. A critical analysis of the available data is presented to provide an overview of the role of the TEs, in phenotypic evolution, especially the evidence of: (a) how stress sensitive storage and release of genetic variation by Hsp90 contribute phenotypic variability by modification of the TEs impact on genome regulation in response to environmental cues?; (b) how the intra-genomic conflicting system is used to generate sex specific development (sexual dimorphism) in Drosophila, in response to sexual selection?; and (c) why interspecific DNA sequence divergence in Drosophila cause deleterious hybrid incompatible phenotypes and how do the evolutionary drivers of the divergence of hybrid incompatibility genes in Drosophila may interact to cause hybrid lethality and sterility? Altogether, the evidences demonstrated that molecular epigenetic mechanisms, tightly linked to TEs, directly affect, alter or interact with the chromatin for changing genome regulation to develop phenotypic variation in Drosophila. [ABSTRACT FROM AUTHOR]

Abstract Background Myelodysplastic neoplasms (MDS) are heterogeneous hematopoietic disorders characterized by ineffective hematopoiesis and genome instability. Mobilization of transposable elements (TEs) is an important source of genome instability leading to oncogenesis, whereas small PIWI-interacting RNAs (piRNAs) act as cellular suppressors of TEs. However, the roles of TEs and piRNAs in MDS remain unclear. Methods In this study, we examined TE and piRNA expression through parallel RNA and small RNA sequencing of CD34+ hematopoietic stem cells from MDS patients. Results Comparative analysis of TE and piRNA expression between MDS and control samples revealed several significantly dysregulated molecules. However, significant differences were observed between lower-risk MDS (LR-MDS) and higher-risk MDS (HR-MDS) samples. In HR-MDS, we found an inverse correlation between decreased TE levels and increased piRNA expression and these TE and piRNA levels were significantly associated with patient outcomes. Importantly, the upregulation of PIWIL2, which encodes a key factor in the piRNA pathway, independently predicted poor prognosis in MDS patients, underscoring its potential as a valuable disease marker. Furthermore, pathway analysis of RNA sequencing data revealed that dysregulation of the TE‒piRNA axis is linked to the suppression of processes related to energy metabolism, the cell cycle, and the immune response, suggesting that these disruptions significantly affect cellular activity. Conclusions Our findings demonstrate the parallel dysregulation of TEs and piRNAs in HR-MDS patients, highlighting their potential role in MDS progression and indicating that the PIWIL2 level is a promising molecular marker for prognosis. Graphical Abstract

Abstract We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.

Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.

Abstract Objectives Despite the advances in genomics, repetitive DNAs (repeats) are still difficult to sequence, assemble, and identify. This is due to their high abundance and diversity, with many repeat families being unique to the organisms in which they were described. In sugar beet, repeats make up a significant portion of the genome (at least 53%), with many repeats being restricted to the beet genera, Beta and Patellifolia. Over the course of over 30 years and many repeat-based studies, over a thousand reference repeat sequences for beet genomes have been identified and many experimentally characterized (e.g. physically located on the chromosomes). Here, we present the collection of these reference repeat sequences for beets. Data description The BeetRepeats_v1.0 resource is a comprehensive compilation of all characterized repeat families, including satellite DNAs, ribosomal DNAs, transposable elements and endogenous viruses. The genomes covered are those of sugar beet and closely related wild beets (genera Beta and Patellifolia) as well as Chenopodium quinoa and Spinacia oleracea (all belonging to the Amaranthaceae). The reference sequences are in fasta format and comprise well-characterized repeats from both repeat categories (dispersed/mobile as well as tandemly arranged). The database is suitable for the RepeatMasker and RepeatExplorer2 pipelines and can be used directly for any repeat annotation and repeat polymorphism detection purposes.

Abstract The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying genome evolution within the Arecaceae family. We sequenced the Chowghat Green Dwarf cultivar, which is resistant to the root (wilt) disease, utilizing Illumina, PacBio, ONT, and Hi-C technologies to produce a chromosome-level genome of ~ 2.68 Gb with a scaffold N50 of 174 Mb; approximately 97% of the genome could be anchored to 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; the BUSCO completeness score was 96.80%, while the k-mer completeness was ~ 87%. The assembled genome includes 2.19 Gb (81.64%) of repetitive sequences, with long terminal repeats (LTRs) constituting the most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in the C. nucifera lineage. A genome-wide analysis of LTR insertion time revealed ancient divergence and proliferation of copia and gypsy elements. In addition, 1368 RGAs were discovered in the CGD genome. We also developed a web server ‘Kalpa Genome Resource’ ( http://210.89.54.198:3000/ ), to manage and store a comprehensive array of genomic data, including genome sequences, genetic markers, structural and functional annotations like metabolic pathways, and transcriptomic profiles. The web server has an embedded genome browser to analyze and visualize the genome, its genomics elements, and transcriptome data. The in-built BLAST server allows sequence homology searches against genome, annotated transcriptome & proteome sequences. The genomic dataset and the database will support comparative genome analysis and can expedite genome-driven breeding and enhancement efforts for tapping genetic gains in coconut.

Abstract Background The centromere is one of the key regions of the eukaryotic chromosome. While maintaining its function, centromeric DNA may differ among closely related species. Here, we explored the composition and structure of the pericentromeres (a chromosomal region including a functional centromere) of Hieracium alpinum (Asteraceae), a member of one of the most diverse genera in the plant kingdom. Previously, we identified a pericentromere-specific tandem repeat that made it possible to distinguish reads within the Oxford Nanopore library attributed to the pericentromeres, separating them into a discrete subset and allowing comparison of the repeatome composition of this subset with the remaining genome. Results We found that the main satellite DNA (satDNA) monomer forms long arrays of linear and block types in the pericentromeric heterochromatin of H. alpinum, and very often, single reads contain forward and reverse arrays and mirror each other. Beside the major, two new minor satDNA families were discovered. In addition to satDNAs, high amounts of LTR retrotransposons (TEs) with dominant of Tekay lineage, were detected in the pericentromeres. We were able to reconstruct four main TEs of the Ty3-gypsy and Ty1-copia superfamilies and compare their relative positions with satDNAs. The latter showed that the conserved domains (CDs) of the TE proteins are located between the newly discovered satDNAs, which appear to be parts of ancient Tekay LTRs that we were able to reconstruct. The dominant satDNA monomer shows a certain similarity to the GAG CD of the Angela retrotransposon. Conclusions The species-specific pericentromeric arrays of the H. alpinum genome are heterogeneous, exhibiting both linear and block type structures. High amounts of forward and reverse arrays of the main satDNA monomer point to multiple microinversions that could be the main mechanism for rapid structural evolution stochastically creating the uniqueness of an individual pericentromeric structure. The traces of TEs insertion waves remain in pericentromeres for a long time, thus “keeping memories” of past genomic events. We counted at least four waves of TEs insertions. In pericentromeres, TEs particles can be transformed into satDNA, which constitutes a background pool of minor families that, under certain conditions, can replace the dominant one(s).

Abstract Background In evolutionary biology, identifying and quantifying inter-lineage genome size variation and elucidating the underlying causes of that variation have long been goals. Repetitive elements (REs) have been proposed and confirmed as being among the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and RE dynamics are not well understood. Results A total of 35 Ensifera insects were collected from different areas in China, including nine species of crickets and 26 species of katydids. The genome sizes of seven species were then determined using flow cytometry. The RepeatExplorer2 pipeline was employed to retrieve the repeated sequences for each species, based on low-coverage (0.1 X) high-throughput Illumina unassembled short reads. The genome sizes of the 35 Ensifera insects exhibited a considerable degree of variation, ranging from 1.00 to 18.34 pg. This variation was more than 18-fold. Similarly, the RE abundances exhibited considerable variation, ranging from 13.66 to 61.16%. In addition, the Tettigonioidea had larger genomes and contained significantly more REs than did the Grylloidea genomes. Analysis of the correlation between RE abundance and the genome size of 35 Ensifera insects revealed that the abundance of REs, transposable elements (TEs), long terminal repeats (LTRs), and long interspersed nuclear elements (LINEs) are significantly correlated with genome size. Notably, there is an inflection point in this correlation, where species with increasingly large genomes (e.g., > 5–10 pg) have repeats that contribute less to genome expansion than expected. Furthermore, this study revealed contrasting evolutionary directions between the Tettigonioidea and Grylloidea clades in terms of the expansion of REs. Tettigonioidea species exhibit a gradual increase in ancestral genome size and RE abundance as they diverge, while Grylloidea species experience sustained genome contraction. Conclusions This study reveals extensive variation in genome size and RE abundance in Ensifera insects, with distinct evolutionary patterns across two major groups, Tettigonioidea and Grylloidea. This provides valuable insights into the variation in genome size and RE abundance in Ensifera insects, offering a comprehensive understanding of their evolutionary history.

Abstract 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.

Abstract Transposable elements (TEs) are often expressed at higher levels in tumor cells than normal cells, implicating these genomic regions as an untapped pool of tumor-associated antigens. In ovarian cancer (OC), protein from the TE ERV-K is frequently expressed by tumor cells. Here we determined whether the targeting of previously identified epitope in the envelope gene (env) of ERV-K resulted in target antigen specificity against cancer cells. We found that transducing healthy donor T cells with an ERV-K-Env-specific T cell receptor construct resulted in antigen specificity only when co-cultured with HLA-A*03:01 B lymphoblastoid cells. Furthermore, in vitro priming of several healthy donors with this epitope of ERV-K-Env did not result in target antigen specificity. These data suggest that the T cell receptor is a poor candidate for targeting this specific ERV-K-Env epitope and has limited potential as a T cell therapy for OC.

Abstract 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.

Abstract The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13–22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31–33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.