Search Results (530)

This critical and selective review synthesizes the accumulating body of biological evidence supporting a process we term epigenetic–genetic coupling as a mechanistic basis for Lamarckian inheritance of somatically acquired adaptations. We propose that evolutionary processes in mammals and higher vertebrates can involve deaminase-driven, reverse transcriptase-mediated, RNA-templated targeted homologous recombination. We contrast well-established examples of “Soft”, reversible epigenetic inheritance with historical and contemporary evidence suggestive of stable, DNA-integrated “Hard” Lamarckian transgenerational inheritance. Our analysis indicates that the establishment of “Hard” Lamarckian inheritance may require specific population dynamics, including inbreeding or interbreeding among phenotypically affected offspring, together with sustained and defined environmental stimuli over one or more generations to consolidate the acquired traits at the genomic level. We also present molecular and cellular evidence supporting RNA-to-DNA genetic feedback mechanisms involving targeted genomic integration, primarily mediated by the DNA repair–associated reverse transcriptase activity of DNA polymerase η. Finally, we review diversification mechanisms in molecular and cellular immunology that now routinely employ single-molecule, real-time, long-read genomic sequencing (6–8 kb). We recommend the broader application of these technologies in future breeding and experimental programs across other somatic systems. Their deployment offers a robust strategy for securing definitive “Hard” molecular evidence of Lamarckian acquired inheritance in diverse biological contexts; including somatically acquired immunity, as well as adaptive behavioral and central nervous system phenotypes. This is compatible with our over-arching goal—to provide an experimental road map of conceptual options to drive future experimentation in acquired inheritance breeding programs. Full article

Cytochrome P450 monooxygenases (CYPs/P450s) play a key role in organisms’ primary and secondary metabolism in species across all domains of life. Accurate annotation of P450 genes is crucial for identifying their functions, evolution, and, consequently, their biotechnological potential. In this study, we report the identification of an unprecedented one-nucleotide exon required for the correct assembly of CYP621A P450 genes from multiple Fusarium species. Through comparative genomic analysis of 20 orthologous CYP621A genes, supported by an intronless CYP621B1 gene from Aspergillus clavatus, we demonstrate that omission of this single-nucleotide exon disrupts exon phase compatibility and prevents reconstruction of a full-length, functional P450 protein. The micro-exon encodes the central nucleotide of the glycine codon in the highly conserved PKG motif, which is essential for maintaining the structural integrity between the EXXR and PERF motifs, a characteristic of P450 enzymes. Importantly, transcriptomic evidence from sequence read archive (SRA) data confirms accurate splicing of this one-nucleotide exon in Fusarium solani and F. acuminatum under multiple growth conditions. This work presents the second example of the smallest exon reported to date for a gene, and the first for a P450 gene or a fungal gene. The study’s findings have broad implications for genome annotation pipelines, underscoring the need for careful manual curation and improved algorithms to detect ultra-small exons in functionally constrained regions of eukaryotic genes. Full article

The Sharpchin Slickhead, Bajacalifornia burragei, is a rarely collected bathypelagic fish endemic to the eastern tropical Pacific Ocean, and its genetic diversity remains undocumented. This study characterizes mitochondrial diversity in a localized deep-basin collection from the Carmen Basin of the Gulf of California by sequencing complete mitochondrial genomes from four individuals collected simultaneously at 1300 m in a single Tucker trawl. A high-quality reference mitogenome was assembled using PacBio HiFi long reads, and three additional mitogenomes were generated from Illumina PE150 libraries mapped to this reference. The mitogenome of B. burragei exhibits the canonical 37 gene architecture and conserved gene order typical of teleost mitogenomes. Overall mitogenome divergence was low (Range: 0.21–0.29%), with most protein-coding and rRNA genes exceeding 99.5% identity. Slightly elevated variation occurred in atp8, nad6, and several tRNA genes. This study provides the first genetic characterization of B. burragei and establishes a baseline for evaluating mitochondrial diversity within a localized collection of individuals and provides a point of comparison for future studies assessing connectivity among deep basins. Full article

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xy_p sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)_n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae. Full article

The mitochondrial (mt) genomes of animals, including humans, are typically a single circular chromosome containing all mt genes. In several animal lineages, however, mt genomes have become fragmented, with genes distributed on multiple minichromosomes. How fragmented mt genomes are transcribed is still poorly understood. In this study, we investigated the transcription of the extensively fragmented mt genomes of the human head louse (Pediculus humanus capitis) and the human body louse (Pediculus humanus corporis). RNA-seq reads of both subspecies were retrieved from the NCBI Sequence Read Archive database and mapped to their mt genomes. The transcription level of each mt gene, minichromosome, motif, coding region and non-coding region, measured by RPKM (Reads Per Kilobase of transcript per Million mapped reads), TPM (Transcripts Per Million) or read coverage, was analysed statistically. In both subspecies, mt minichromosomes were transcribed entirely, with coding regions transcribed at much higher levels than non-coding regions. The 37 mt genes are transcribed unevenly, with rrnL, cox1, cox2, cox3 and atp6 transcribed at significantly higher levels than several other genes. Many transcription events terminate near a GC-rich motif in the non-coding regions; however, some transcription events pass this motif, leading to the transcription of entire non-coding regions. Despite the drastic difference in mt genome organisation, the human lice share several transcriptional features with humans, but also have unique features related to their fragmented mt genome organisation. The current study represents the first effort into the transcription of fragmented mt genomes. As more RNA-seq data become available, further studies on other animals with fragmented mt genomes are necessary to fully understand how genome fragmentation affects transcription. Full article

The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice. Full article

Chikungunya virus (CHIKV) poses an increasing global public health threat, as evidenced by the significant 2025 Foshan outbreak in China. Rapid, whole-genome sequencing (WGS) is critical for outbreak response but is challenged by primer mismatches across diverse lineages and a lack of direct sequencing platform comparisons. To address this, we developed a novel lineage-inclusive primer set and performed parallel WGS on 24 clinical samples from the outbreak using both Illumina (NGS) and Oxford Nanopore Technologies (TGS) platforms. Our lineage-inclusive primer set successfully amplified full-length CHIKV genomes across all samples. Comparisons revealed that Illumina NGS provided higher raw read accuracy, while Nanopore TGS achieved more complete coverage of terminal UTRs with a faster turnaround time. Crucially, after polishing, variant calls between the two platforms were 100% concordant. Phylogenetic analysis was consistent with a single introduction event, with all outbreak isolates forming a monophyletic clade within the ECSA lineage most closely related to contemporaneous strains from Réunion Island. This study validates a lineage-inclusive amplicon-based sequencing strategy and demonstrates that NGS and TGS offer complementary advantages. When integrated, they provide a robust framework for real-time genomic surveillance, enhancing preparedness and guiding public health interventions against CHIKV. Full article

Background/Objectives: Non-invasive samples offer an attractive alternative to logistically challenging invasive approaches in wildlife genetic studies but often contain low-quality host DNA that limits downstream analyses. Here, we assessed the applicability of moulted Eurasian goshawk feathers as a DNA source for whole-genome re-sequencing. Methods: We analysed 75 moulted feathers collected opportunistically from breeding territories. Each feather was measured from tip to tip, and its condition was visually assessed. Whole-genome re-sequencing was performed with a target coverage of 13× using 150 bp paired-end reads. Results: Feathers yielded an average of 7.19 ± 10.93 ng/μL DNA. DNA yield was positively correlated with feather size and the presence of blood traces in the calamus. On average, feather samples performed well, producing 208.7 ± 59.82 million reads, of which 82.69 ± 27.15% aligned to the reference genome, resulting in 83.58 ± 19.02% of the genome being covered at least once. After quality filtering, 10.34 ± 3.11 million biallelic single-nucleotide variants remained, of which 457,745 were common variants (MAF > 0.05). Larger feathers in good condition, with higher DNA yields and blood traces in the calamus, tended to perform better throughout the re-sequencing workflow. Nevertheless, approximately 22.7% of samples failed due to high missing data or poor genotype quality. Conclusions: Performance varied substantially even among samples with similar characteristics, indicating that improved sample selection incorporating direct measures of host DNA quality may be beneficial. Despite these challenges, moulted feathers represent a readily available DNA source for genome-wide re-sequencing of medium- to large-sized raptor species. Full article

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by irreversible cognitive decline and synaptic dysfunction and represents the most prevalent etiology of dementia, accounting for an estimated 60–70% of all clinically diagnosed cases worldwide. The growing focus on microglia–neuron interactions in AD research highlights their diverse, region-specific responses, which are driven by the functional and pathological heterogeneity across different brain regions. Therefore, investigating the interactions between microglia and neurons is of crucial importance. To explore the regional heterogeneity of microglia–neuron crosstalk in AD, we integrated human single-nucleus RNA sequencing data from the prefrontal cortex (PFC), hippocampus (HPC), and occipital lobe (OL) provided by the ssREAD database. Our study delineated four microglial subtypes and uncovered a pseudotime trajectory activation trajectory leading to the disease-associated microglia (DAM) phenotype. The transition along this trajectory is driven and stabilized by a key molecular switch: the coordinated downregulation of inhibitory factors (e.g., LINGO1) and upregulation of immune-effector and antigen-presentation programs, which collectively establish the pro-inflammatory DAM state. Furthermore, we observed that each brain region displayed unique microglia–neuron communication patterns in response to AD pathology. The PFC and OL engage a THY1-ITGAX/ITGB2 signaling axis; the HPC predominantly utilizes the PTPRM pathway. Notably, THY1 dysregulation strongly correlates with pathology in the PFC, HPC, and OL, suggesting that microglia–neuron crosstalk in AD possesses both heterogeneity and commonality. The main contribution of this study is the systematic characterization of region-specific microglia-neuron interactions and the identification of THY1 as a potential mediator that may be targeted therapeutically to modulate microglial function in affected brain regions. Full article

The family Flaviviridae has been expanded to include the highly divergent flavi-like viruses into three new families, Flaviviridae, Pestiviridae, and Hepaciviridae, in the order Amarillovirales. Classical flavivirids are small, enveloped viruses with positive-sense ssRNA genomes lacking a 3′ poly(A) tail and ~9.0–13.0 kb in length, with a single open reading frame (ORF) encoding structural proteins at the N-terminus and nonstructural proteins at the C-terminus. Members infect a wide range of mammals, birds, and insects, and many are host-specific and pathogenic. Although the RNA-directed RNA polymerase (RdRP) gene sequences of the flavi-like viruses group phylogenetically with those of classical flavivirids, flavi-like viruses often encode larger polyproteins and possess substantially longer genomes of up to ~40 kb, and some have a 3′ poly(A) tail. Their host range extends across the whole animal kingdom and angiosperm plants. This review describes the reported flavi-like viruses of aquatic animals, providing a meaningful update on all three new families in Amarillovirales that have been discovered using metagenomics in fish, crustaceans, mollusks, and echinoderms. These amarilloviruses include pathogenic viruses of aquatic animals, such as Cyclopterus lumpus virus (CLuV) detected in moribund lumpfish, and infectious precocity virus (IPV) found in iron prawn syndrome (IPS)-affected farmed giant freshwater prawns. Full article

Fusion-associated small transmembrane (FAST) proteins are viral nonstructural proteins known to be encoded by specific members of the Spinareoviridae, specifically within the Aquareovirus and Orthoreovirus genera. These proteins specialize in mediating cell–cell fusion, leading to syncytia. Unlike enveloped viruses, naked viruses do not rely on fusion proteins for cell entry; however, such proteins may facilitate viral spread between cells. Although not essential for virus replication, FAST proteins have been shown to enhance viral replication, particularly during the early stages of infection. More recently, proteins with characteristics resembling FAST proteins have been identified in a broader range of viruses, including several rotavirus species within the family Sedoreoviridae, and, unexpectedly, in some enveloped viruses within the Coronaviridae family. Here, we present protein sequence analyses suggesting that viruses of the recently established virus family Pistolviridae (order Ghabrivirales) also encode proteins with similarity to FAST proteins. Pistolviruses are small double-stranded RNA viruses that infect piscine species, and were initially referred to as “toti-like” viruses due to genomic similarities with members of the former Totiviridae, which infect single-celled organisms. The putative FAST proteins of the pistolviruses may be expressed either from small, distinct open reading frames or suggested to be produced as cleavage products derived from polyproteins. Full article

Pleurotus ostreatus, a globally cultivated oyster mushroom, is susceptible to viral infections that threaten yield and quality. This study reports the identification and characterization of three novel viruses from a symptomatic P. ostreatus strain K3: Pleurotus ostreatus deltaflexivirus 2, 3, and 4 (PoDFV2, PoDFV3, PoDFV4). Complete genome sequencing revealed that they are single-stranded, positive-sense RNA viruses with lengths of 7809 nt, 7771 nt, and 7786 nt, encoding 5, 2, and 4 open reading frames (ORFs), respectively. The largest open reading frame (ORF1) encodes a putative replication-associated polyprotein (RP) containing three conserved domains—viral RNA methyltransferase (Mtr), viral RNA helicase (Hel), and RNA-dependent RNA polymerase (RdRp). Based on genomic sequence analysis, multiple sequence alignments, and phylogenetic analysis, PoDFV2–4 were identified as novel viruses of the genus Deltaflexivirus within the family Deltaflexiviridae. PoDFV2–4 had no significant effects on mycelial growth rate, plate mycelial biomass, or laccase activity. However, they significantly inhibited mycelial cellulase activity and resulted in malformed fruiting bodies, as well as a substantial reduction in yield. Full article

Single nucleotide variants (SNVs) are crucial in cancer occurrence and development. SNVs at the transcriptomic level generally come from genomic variants (g-tSNVs) and RNA editing (e-tSNVs). The types and quantities of e-tSNVs remain a subject of debate due to a relatively poor understanding of RNA editing processes. Herein, we developed TSCS (Transcript SNVs Classifier relying on complementary sequencings), a machine learning classifier that integrates short-read (MGI) and long-read (PacBio) RNA-seq data to accurately distinguish true transcript SNVs using stringent criteria. Applied to five colorectal cancer cell lines (HCT15, LoVo, SW480, SW620, and HCT116), TSCS demonstrated superior accuracy and sensitivity, outperforming established tools (GATK, BCFtools, Longshot, RED_ML). It increased the total detected transcript SNVs by 31.83% on average, with g-tSNVs and e-tSNVs exceeding conventional methods by >1-fold and >2-fold, respectively. TSCS achieved mean recall rates of 75.3% for g-tSNVs and 77.2% for e-tSNVs. Notably, for the first time, e-tSNVs were found in a relatively large proportion of total transcript SNVs in cancer cell lines, approximately 40%. Of the identified e-tSNVs, 80% were attributed to the known RNA editing, but the other e-tSNVs did not fall into any known category. Importantly, the e-tSNVs uniquely detected in this study showed distinct patterns in SNV types and genomic locations. Additionally, the transcript SNVs called by TSCS were partially confirmed using experimental approaches, such as Sanger sequencing, RNC-seq, and mass spectrometry. This study lays the foundation for surveying and appraising the cancer-related e-tSNVs. Full article

Potyvirus genomes are expressed as a single large open reading frame, which is translated into a polyprotein that is post-translationally cleaved by three virus-encoded proteases into 10 functional proteins. Several of these potyviral proteins, including nuclear inclusion protein b (NIb), are multifunctional. Here, using the classic GFP silencing in Nicotiana benthamiana gfp-transgenic plants, we show that potato virus Y (PVY) NIb, in addition to its canonical role as the viral RNA-dependent RNA polymerase (RdRP), functions as a suppressor of RNA silencing. Mutational analyses reveal a previously unreported NIb nuclear localization signal (NLS) consisting of a triple-lysine motif. NIb suppression of RNA silencing activity was lost when the NLS was mutated, suggesting that nuclear localization is required for NIb suppression of RNA silencing activity. Analysis of sequenced GFP siRNAs revealed three reproducible hotspot regions at ≈175 nt, ≈320–330 nt, and a broader 3′-proximal region spanning ≈560–700 nt that contains multiple local maxima. These data show differences in the positional distribution of siRNAs between samples expressing NIb and those expressing NIb^Del3×2, the NIb null mutant that does not suppress RNA silencing. However, the positional distribution of GFP-derived small RNAs across the transgene differed modestly between NIb and NIb^Del3×2, while both treatments showed the same three reproducible hotspot regions. Furthermore, NIb was found to interact with four key RNA silencing pathway proteins—AGO4, HSP70, HSP90, and SGS3. Except for HSP90, each of these proteins showed degradation products that were absent in NIb mutants that did not suppress RNA silencing. These findings support a role for NIb in countering host defense during virus infection. Full article

This study explores the virome of fifteen peanut cultivars in Korea. Through RNA sequencing, 305 viral contigs associated with cucumber mosaic virus (CMV), peanut mottle virus (PeMoV), bean common mosaic virus (BCMV), and brassica yellows virus (BrYV) were identified, with CMV notably prevalent across samples. Evaluation of viral abundance using viral reads and TPM values revealed CMV dominance in reads and PeMoV prominence in normalized values in select samples. Complete genomes of BCMV, PeMoV, BrYV, and CMV segments were assembled, enabling phylogenetic analysis that uncovered genetic relationships among viral isolates. RT-PCR confirmed BCMV, CMV, and PeMoV presence. Genetic diversity within BCMV was evident through single-nucleotide polymorphism (SNP) analysis, displaying diverse patterns and correlations with viral reads. This study discusses the implications for peanut cultivation, stressing the importance of ongoing research to manage viral diseases. It forms a foundational resource for future investigations into peanut virology, guiding strategies for disease management in peanut crops. Full article