Search Results (196)

Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the industry. Here, we integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C) technologies to assemble the first chromosome-level reference genome of R. dybowskii. The final assembled genome size is 3.77 Gb, with a contig N50 of 16.27 Mb and a scaffold N50 of 41.54 Mb. A total of 97.82% of the sequences were successfully anchored onto 12 definitive pseudochromosomes corresponding to haploid chromosome number. Repetitive elements account for 65.61% of the genome, characterized by an unusual dominance of DNA transposons (37.19%) over retrotransposons, suggesting a genomic landscape shaped by extreme cold adaptation. Combining multi-tissue transcriptomic evidence, we structurally predicted 26,862 protein-coding genes, and the predicted gene set showed a BUSCO completeness of 96.1%. Functional annotation successfully categorized 96.55% of the total genes. This genomic resource successfully fills a crucial phylogenetic gap in the Rana genus, driving high-efficiency molecular breeding and sustainable conservation of this economic amphibian. Full article

Mutator-like elements (MULEs) are a major DNA transposon superfamily. The evolutionary profiles of MULE transposons and their impact on arthropod genomes remain largely unexplored. Here, we define the evolutionary landscape—including distribution, diversity, structure, and activity—of MULE transposons across 4268 assembled arthropod genomes. Systematic analysis reveals a divergent evolutionary profile. From the sampled genomes, 222 arthropod species harbor MULE transposons, comprising 322 distinct elements. Phylogenetic analysis divides arthropod MULE transposons into twelve clades. The majority of species (164) carry only one type of MULE transposon, while 51 species contain two or three types, and a few host multiple types (4–9). Copy numbers vary significantly, ranging from 5 to 88 per species. Structural variation is pronounced: full-length MULEs range from 1.4 kb to 10.0 kb, with most falling between 2.5 kb and 5.0 kb. Low Kimura divergence in several species suggests recent MULE activity, noteworthy because most transposons are expected to be inactive. Collectively, our results show that MULEs are widely distributed yet phylogenetically structured across arthropods, with lineage-specific expansions and recent activity in several species. Full article

DNA methylation, the covalent addition of methyl groups to cytosine (5mC) or adenine (6mA) in DNA, is a fundamental mechanism of epigenetic inheritance conserved from bacteria to humans. Fungi provide a uniquely informative window into the evolutionary logic of methylation systems. Spanning more than 1 billion years of diversification, the kingdom encompasses species that have lost cytosine methylation entirely, lineages that use 5mC to silence transposons and drive the irreversible genome-defense process known as repeat-induced point mutation (RIP), and early-diverging lineages, in which 6mA has emerged as a prominent chromatin mark. The methyltransferases underlying these strategies (DIM-2, RID, DNMT1-RFD, DNMT5, and the MT-A70 complex) and the recently characterized demethylases Dmt1 and CcTet are structurally and mechanistically distinct from their mammalian counterparts. Here we review the mechanisms, targets, and biological functions of fungal DNA methyltransferases and demethylases, incorporating cryo-EM structural insights into DIM-2 and DNMT5 catalysis, analyses of DNMT gene loss as a continuous evolutionary process, the antiviral role of DIM-2 in vegetative hyphae, and the emerging model of 6mA as a heritable regulatory mark in early-diverging lineages. By integrating these advances, this review offers the updated and comprehensive account of DNA methylation across fungi. Full article

Root knot nematodes (RKNs) induce galls, containing multinucleated giant cells (GCs) to nourish them. The differentiation of precursor cells to galls/GCs involves extensive cellular reprogramming with multiple layers of regulation. Epigenetic regulation during the early stages of infection indicates that RNA-directed DNA methylation (RdDM) and microRNA-dependent gene silencing contribute to transcriptional and post-transcriptional reprogramming during gall organogenesis. Although later stages of galls/GC development are crucial for nematode life-cycle maintenance, epigenetic reprogramming events remain largely unexplored. An integrative analysis of sRNAs, DNA methylation, and transcriptomic dynamics in galls induced by Meloidogyne javanica revealed that enrichment of 24 nt sRNAs represents a gall hallmark across early and late developmental stages. Fewer gall-distinctive sRNAs were detected at mid-to-late stages than at early stages, alongside a pronounced spatial reorganization of rasiRNA accumulation. At early stages, gall-distinctive rasiRNAs preferentially accumulated in pericentromeric retrotransposon-rich regions, whereas, at mid-to-late stages, they predominantly localized to chromosome arms, matching DNA transposons, promoters, and gene bodies. A decline in the regulatory influence of miRNAs was observed as infection progressed, possibly reflecting a transition toward specialized regulatory states associated with gall maintenance. Moreover, three regulatory modules, miR2111-5p/HOLT, miR172/AP2, and miR156/SPL10, were tightly but oppositely regulated at 3 and 14 days post-infection. Furthermore, miR156/SPL10 showed crucial functions during gall formation and/or maintenance, possibly influenced by hormonal cues involving ARF8 among other ARFs. Our results highlight stage-specific patterns involving sRNA dynamics, DNA methylation, and transcriptomic changes underlying nematode feeding site development and maintenance. Full article

This study presents a high-quality chromosome-level genome assembly of Morchella sextelata (54.64 Mb, 26 pseudochromosomes) and systematically characterizes its genomic and evolutionary features. Phylogenetic analysis indicates that M. sextelata diverged early within the Morchella genus (~14.2 million years ago) and underwent substantial genomic remodeling, with 1124 expanded and 1961 contracted gene families. Enrichment analysis of rapidly expanded gene families highlights two prominent functional themes: genes associated with small molecule/ion binding and secondary metabolite biosynthesis, and genes linked to the Fanconi anemia pathway and DNA repair/recombination. Notably, 56.96% of the COG-annotated M. sextelata-specific genes encode retrotransposon-related proteins, and this enrichment coincides with the expansion of DNA repair systems—a pattern reminiscent of the “transposon domestication” model. Functional genomic analyses further reveal that the glycoside hydrolase system is dominated by GH5, GH43, and GH3 families, suggesting a predicted capacity for plant cell wall polysaccharide degradation, while 12 biosynthetic gene clusters indicate genetic potential for terpenoid and non-ribosomal peptide biosynthesis. These findings provide a valuable genomic resource for M. sextelata and offer new insights into the role of transposable element mediated remodeling in fungal genome evolution. Full article

The parasitic wasps of Aphelinidae (Hymenoptera) are a group of insects with significant biological control value. However, their genomic evolution and ecological adaptation mechanisms remain unclear. In this study, we focused on the genome analysis of Eretmocerus hayati and performed a comparative analysis with four other species from Aphelinidae. Our results indicated that the divergence time of Aphelinidae was approximately 119.9 million years ago. In Er. hayati, gene families related to energy metabolism and humoral immunity have significantly expanded, which may be associated with the high metabolic demands of its small body size and the immune adaptation strategies resulting from its unique parasitic methods. Additionally, genes involved in DNA replication and recombination have undergone positive selection in the ancestral branch of Aphelinidae species. Compared with 23 species within nine families in the Chalcidoidea superfamily studied here, the genome size of Er. hayati is the largest. The analysis of repetitive sequences revealed a recent burst of long terminal repeat (LTR) sequence insertions in the genome of Er. hayati. Our study indicates the evolutionary characteristics of Er. hayati in terms of gene family evolution, chromosomal collinearity, and transposon dynamics, providing a theoretical basis for understanding the environmental adaptation and biological control applications. Full article

Large DNA fragment deletion (LDFD) provides a powerful means to reconfigure plant genomes at the kilobase to megabase scale, enabling the dissection of genome function, elucidation of non-coding regulatory elements, modulation of gene dosage, reorganization of chromosomal architecture, and implementation of synthetic biology designs. In this review, we systematically compare the mechanisms, efficiencies, advantages, and limitations of the major LDFD technologies that have been applied in plants, including ZFNs, TALENs, CRISPR/Cas systems (Cas9, Cas12a, Cas3), site-specific recombinases, transposon-based systems, and prime editing-derived strategies. We highlight how plant-specific features of chromatin organization and DNA repair constrain large deletions, and discuss the current bottlenecks in achieving efficient, precise, and predictable LDFD across diverse crop genomes. Finally, we outline future directions for plant LDFD, emphasizing AI-assisted design of nucleases and recombinases, protein-directed evolution, and improved DNA- and RNP-based delivery systems. Together, these advances are expected to transform LDFD from a specialized tool into a broadly accessible platform for functional genomics, trait engineering and rational genome design in plants. Full article

The presence of an extra DNA segment in a genome could indicate a transposon or another repetitive element on the move. In Neurospora crassa, a surveillance mechanism called meiotic silencing by unpaired DNA (MSUD) is maintained to monitor these selfish elements. MSUD utilizes common RNA interference (RNAi) factors, including the SMS-2 Argonaute, to target mRNAs from genes lacking a pairing partner during meiosis. In eukaryotes, an mRNA transcript is typically bound at the 5′ cap by the cap-binding complex (CBC), which assists in its nuclear export. Previously, we discovered that CBC and its interactor NCBP3 mediate MSUD, possibly by guiding the perinuclear SMS-2 to effectively recognize exported mRNAs. Here, we report that ARS2, a CBC cofactor, is involved in MSUD. ARS2 interacts with both CBC and NCBP3, and it may help bring them together. In addition to its role in silencing, ARS2 also contributes to vegetative growth and sexual sporulation. Full article

Mobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their mobilization. To address this question, we examined LTR-RTE activation in Arabidopsis thaliana, Brassica napus, and Nicotiana benthamiana following infection with the RNA viruses Tobacco rattle virus (TRV), Potato virus X (PVX), and Tobacco ringspot virus (TRSV). Nanopore cDNA sequencing revealed virus-specific transcriptional responses, with PVX uniquely triggering a strong transcriptional burst of diverse LTR-RTE families in N. benthamiana. To test the role of viral suppressors of RNA silencing (VSRs) in this process, we analyzed extrachromosomal circular DNA (eccDNA) from plants infected with TRV expressing the VSR P19. This analysis identified eccDNA derived from Ty3/Gypsy Galadriel elements, demonstrating that viral infection can promote not only retrotransposon transcription but also eccDNA production, which may indicate the ability of LTR-RTEs to transpose. These findings clearly illustrate that plant–virus interactions can induce not only changes in gene transcription, but also the activation of multiple retrotransposons, highlighting a potential evolutionary interface linking antiviral defense and transposon regulation. Full article

In this study we employed nanopore whole genome sequencing to analyze the resistance genes, genomic islands and prophage DNA in two multidrug resistant E. rhusiopathiae strains, i.e., 670 and 147, isolated from domestic geese. MLST profiles and core-genome phylogeny were determined to assess strain relatedness. In strain 670 (serotype 8, ST 113), a novel 53 kb prophage φEr670 carrying the lnuB and lsaE resistance genes was identified. Regions highly homologous to the φEr670 prophage were detected in 36 of 586 (6.14%) publicly available E. rhusiopathiae genomes, as well as in some other Gram-positive bacteria, and usually contained resistance genes. E. rhusiopathiae strain 147 (serotype 5, ST 243) was found to contain a composite 98 kb genomic island (GI_Er147) carrying the ant(6)-Ia and spw genes, as well as gene encoding a putative lincosamide nucleotidyltransferase designated lnu(J) and a vat family gene encoding a putative streptogramin A O-acetyltransferase. The lnu(J) gene exhibited 83.6% homology to the lnu(D) gene, and lnu(J)-positive E. rhusiopathiae strains displayed intermediate susceptibility to lincomycin. Vat-positive strain 147 and vat-negative E. rhusiopathiae strains showed similar susceptibility to quinupristin/dalfopristin. The presence of the Tn916 transposon carrying the tetM gene was confirmed in the genomes of both E. rhusiopathiae strains; in strain 147, however, Tn916 was located within ICEEr1012. Based on analyses of additional E. rhusiopathiae genomes, the integration sites of Tn916, ICEEr1012, and GI_Er147 were identified as genomic “hot spots,” contributing to the genome plasticity of E. rhusiopathiae. Prophage φEr670 and GI_Er147 as well as the Tn916 transposon and ICEEr1012 are most likely responsible for the dissemination of resistance genes in E. rhusiopathiae. Prophages highly homologous to φEr670 act as carriers of resistance genes in various Gram-positive bacteria. However, the transferability of the identified genetic elements and the functional role of the lnu(J) gene require further investigation. This study provides new insights into the diversity of MGEs in E. rhusiopathiae and advances understanding of the genomic mechanisms driving antimicrobial resistance in Gram-positive bacteria. Full article

Background/Objectives: The PB family of “cut-and-paste” DNA transposons shows great promise as genetic manipulation tools while significantly impacting eukaryotic genome evolution. However, their evolutionary profile in beetles (Coleoptera), the most species-rich animal order, remains poorly characterized. Methods: A local tBLASTN search was conducted to mine PiggyBac (PB) transposons across 136 coleopteran insect genomes, using the DDE domain of the PB transposase as the query. Multiple sequence alignment was performed with MAFFT, and a maximum likelihood phylogenetic tree of the transposase DDE domains was constructed using IQ-TREE. Evolutionary dynamics were analyzed by means of K-divergence. Results: Our study reveals PB transposons are widely distributed, highly diverse, and remarkably active across beetles. We detected PB elements in 62 of 136 examined species (45%), classifying them into six distinct clades. A total of 62 PB-containing species harbored intact copies, with most showing recent insertions (K divergence ≈ 0), indicating ongoing transpositional activity. Notably, PB elements from Harmonia axyridis, Apoderus coryli, and Diabrotica balteata exhibit exceptional potential for genetic tool development. Structurally, intact PB elements ranged from 2074 to 3465 bp, each containing a single transposase ORF (500–725 aa). All were flanked by terminal inverted repeats and generated TTAA target site duplications. Conclusions: These findings demonstrate PB transposons have not only shaped historical beetle genome evolution but continue to drive genomic diversification, underscoring their dual significance as natural genome architects and promising biotechnological tools. Full article

Epigenetic DNA modification is a key component of the defense system against invading nucleic acids such as transposons. TET/JBP dioxygenases oxidize 5-methylcytosine and lead to its replacement by cytosine in mammals. Expansion of TET/JBP genes and their association with DNA transposons were previously reported in Basidiomycota fungi. In this study, a thorough bioinformatics investigation of TET/JBP genes revealed that diverse groups of DNA transposons have captured a TET/JBP dioxygenase in three lineages of fungi: Pucciniomycetes (rusts) and Agaricomycetes (mushrooms) in Basidiomycota, and Pezizomycetes (morels and truffles) in Ascomycota. TET/JBP genes encoded by DNA transposons can be classified into three types, designated as PU, AG, and PE here. The PU type is distributed in Pucciniomycetes and encoded by seven different lineages of DNA transposons (Dileera, hAT, Harbinger, IS3EU, EnSpm, ESTA, and Helitron). The AG type is distributed in Agaricomycetes, and encoded by two lineages of DNA transposons (Kyakuja and Zisupton). The PE type is distributed in Pezizomycetes and Agaricomycetes, and encoded by five lineages of DNA transposons (Zisupton, IS3EU, EnSpm, Plavaka, and Helitron). Phylogenetic analysis indicated several transmission events from certain DNA transposon lineage to another. These transposon-encoded TET/JBP dioxygenases likely contribute to the escape of transposons from the methylation-based silencing system in fungi. Full article

Background/Objectives: Germline BRCA1 mutations account for ~15–20% of hereditary breast and ovarian cancer (HBOC) cases. While most are small sequence variants, structural rearrangements also contribute significantly to the pathogenic landscape. Conventional diagnostic workflows often miss such events, underscoring the need for comprehensive approaches. Here, we report a previously undescribed pathogenic mechanism—a transposon-mediated processed transcript insertion—expanding the mutational spectrum underlying hereditary breast cancer susceptibility. Methods: The studied case was discovered during our germline genotyping routine: next-generation sequencing followed by library preparation with a custom hereditary cancer panel. The identified variant was validated by orthogonal sequencing and multiplex ligation-dependent probe amplification (MLPA). RNA-level functional assays, including nonsense-mediated decay inhibition, were conducted to assess transcript stability. Constitutional origin was confirmed by analysis of multiple normal tissues, and tumor material was evaluated for loss of heterozygosity (LOH). Results: NGS detected a 700 bp insertion in exon 16 of BRCA1, corresponding to a complete processed transcript of RPL18A. The insertion caused a frameshift and premature stop codon, triggering degradation of the aberrant transcript. The variant was present in multiple somatic tissues, and its heritable nature was further confirmed by genotyping a first-degree relative, who was also found to carry the insertion. Tumor DNA analysis revealed strong LOH with retention of the variant allele. Conclusions: This study identifies, for the first time, a heritable processed transcript insertion as a pathogenic event in BRCA1. Such variants are undetectable by conventional diagnostic workflows lacking structural variant analysis, highlighting the importance of comprehensive approaches for accurate diagnosis and genetic counselling in hereditary cancer syndromes. Full article

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and play essential roles in genome stability, gonadal development, and gametogenesis in animals. The Japanese flounder (Paralichthys olivaceus) is an important marine culture teleost in North Asia, showing pronounced sexual size dimorphism, where gynogenetic induction of all-female cohorts can markedly enhance production. However, the PIWI/piRNA pathway in gynogenetic diploid P. olivaceus, which often exhibit gonadal dysgenesis, poor gamete quality, and low fertilization rates, remains poorly understood. In this study, RNA-seq and small RNA-seq data from 11 tissues and 6 developmental stages of common P. olivaceus, as well as the gonads of gynogenetic P. olivaceus, were analyzed to characterize the PIWI/piRNA pathway and its roles in transposon and gene regulation within the germline. The results showed that PIWI/piRNA genes were predominantly expressed in gonads and early embryogenesis in common P. olivaceus, with the highest expression in testis. Clustered piRNAs were identified in the testis and early embryos of common P. olivaceus, which targeted multiple transposon and gene families. Intriguingly, gynogenetic P. olivaceus gonads harbored abundant clustered piRNAs not only in the testes but also in the ovaries, both targeting similar transposon families as that in common P. olivaceus. Notably, the DNA transposon Tc1/Mariner family and pim genes were the most heavily targeted by piRNAs in gynogenetic P. olivaceus, with testis-biased expression. Expanded pim genes were identified in P. olivaceus, overlapping with piRNA clusters, and the in vitro test in P. olivaceus testes revealed that the expanded pim genes may be pseudogenes as a piRNA cluster reference to generate piRNAs regulating the conventional pim members. These unique features of the PIWI/piRNA pathway in gynogenetic diploid P. olivaceus may underline their impaired reproductive ability, and have important theoretical and practical implications for teleost gynogenetic breeding. Full article