Search Results (66)

The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi. Full article

Thelazia callipaeda is a vector-borne zoonotic eyeworm infecting companion animals, wildlife, and humans, but chromosome-scale genomic resources from Chinese clinical material remain limited. We generated a genome supported by Pacific Biosciences (PacBio) high-fidelity (HiFi) sequencing and high-throughput chromosome conformation capture (Hi-C) from 100 adult worms recovered from naturally infected dogs in Beijing and compared its chromosome-scale organization with Portuguese assembly GCA_965194785.1. The final assembly spans 119.53 megabases (Mb) and comprises 115 top-level sequences, including four pseudomolecules totaling 91.26 Mb (76.34%) and 111 unanchored sequences. Genome-mode Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis recovered 98.5% complete chromadorean orthologues, and the representative 11,788-protein gene set recovered 92.6%. Sequence-level alignment resolved Chinese chromosomes 1–4 (chr1–chr4) to Portuguese chr1, chrX, chr3, and chr2, respectively, with retained alignments covering 95.9–99.2% of each Chinese pseudomolecule and estimated sequence identities of 99.75–99.91%. Strong chromosome-scale collinearity was accompanied by localized reverse-collinear regions, including 0.243 Mb and 0.115 Mb intervals on chr2–chrX and chr3–chr3. The anchored sequences contained 96.7% of predicted genes and were substantially more gene-dense than the unanchored sequences. These results establish a clinically sourced Chinese chromosome-scale reference and provide a validated framework for future individual-worm, population-genomic, structural-variation, and comparative genomic studies of this parasite. Full article

Background/Objectives: The long-spined sea urchin Diadema antillarum is a keystone herbivore whose grazing maintains Caribbean coral reefs; basin-wide mass mortalities in 1983–1984 and 2022 have made genomic resources a conservation priority, yet no nuclear genome existed for the species. We aimed to generate the first nuclear reference and to resolve the high heterozygosity that complicates genome assembly in broadcast-spawning marine invertebrates. Methods: For the assembly, we combined PacBio HiFi, Oxford Nanopore, and Illumina sequencing. Genome size and heterozygosity were estimated by k-mer profiling. We compared standard and haplotype-aware assembly strategies (hifiasm), evaluated completeness with BUSCO, and annotated repeats using a species-specific RepeatModeler library. Results: k-mer profiling estimated a haploid genome of ~703 Mb with 2.52% heterozygosity. Standard assembly then produced an inflated 1.75 Gb assembly (98.4% BUSCO-complete but 84.4% duplicated), indicating retention of both haplotypes. Haplotype-aware reassembly separated this into a collapsed primary assembly (1.03 Gb) and two phased haplotypes (0.95 and 0.89 Gb), each comparable in size to the chromosome-level congener D. antillarum (886 Mb). BUSCO completeness reached 99.0%, with single-copy orthologs rising to 85–90%, and reference-free consensus quality reached QV 44.5 (Merqury; initial assembly). This genome is repeat-rich (42.84% repetitive; 29.96% unclassified). Conclusions: We provide the collapsed primary assembly together with both phased haplotypes as a haplotype-resolved reference for D. antillarum, establishing a foundation for immunogenomic, comparative, and population-genetic studies and for monitoring and restoration of this ecologically critical species. More broadly, the study shows that haplotype-aware assembly is essential for resolving such highly heterozygous genomes and delivers the genomic foundation needed to guide the conservation of this keystone Caribbean reef species. Full article

Characterizing the mosquito virome is essential for understanding host–microbiota interactions and vector competence, but it can be influenced by sample scale, sequencing strategy, and host depletion. This study evaluated the effect of sampling scale on mosquito virome characterization using a third-generation sequencing (TGS) metagenomics approach based on PacBio HiFi long reads, applied to L4 larvae and adults of Aedes mariae, analyzing single individuals and pools of increasing size before and after host genome removal. The results showed that sequencing yield did not increase with pool size, indicating that the total number of reads is not proportional to the number of individuals. Host genome removal reduced the overall number of reads but altered their composition, increasing the relative proportion of assigned viral reads and reducing unclassified sequences. Despite a similar total read output, virome diversity increased with pool size, with larger pools showing greater taxonomic richness driven by the contribution of each individual. However, the high proportion of unassigned reads suggests the presence of uncharacterized viruses. This methodological workflow was technically feasible for both single-individual and pooled samples. Single-individual analyses may provide complementary information on individual-level virome composition and on low-abundance viral taxa that could be less apparent in pooled samples, whereas pooled samples may facilitate the detection of a broader range of viral taxa and may better capture the shared component of viral diversity within the analyzed population. Full article

Molecular characterization of the transferred DNA (T-DNA) insertion sites is required for the safety assessment of genetically modified (GM) crops, yet conventional PCR-based methods are labor-intensive and limited in their ability to resolve complex structural variations. We present T-DNA Analyzer, an integrated bioinformatics pipeline that transforms long-read sequencing data (PacBio HiFi or Oxford Nanopore) into a comprehensive insertion site report. The pipeline implements a host-derived read filter that subtracts host-homologous vector regions to eliminate false-positive chimeric read calls; a multi-segment fusion detection algorithm that resolves complex T-DNA integration architectures; and a deletion gap gene impact analysis that identifies genes affected by host genome deletions at the integration site. Validation on maize and cotton datasets demonstrated that the host-derived filter excluded 86.4% of false-positive reads while retaining all true chimeric reads, and the fusion detection algorithm successfully reconstructed a two-copy tandem T-DNA repeat within a single long read. T-DNA Analyzer provides automated, reproducible molecular characterization designed to support regulatory molecular characterization and is freely available as open-source software. Full article

The Arabian leopard (Panthera pardus nimr), native to the Arabian Peninsula, is critically endangered and faces acute threats from habitat fragmentation, low population size, and genetic erosion. As a continuation of our previous study on the complete mitochondrial genome of this subspecies, we now report the first nuclear genome assembly of P. p. nimr, generated from the same wild-born male individual sampled in the Oman. Using PacBio HiFi long-read sequencing, we produced 162.9 gigabases (Gb) of high-fidelity data and assembled a haplotype-aware draft genome with HiFiasm. The assembly spans approximately 2.43 Gb across 94 contigs, achieving a contig N50 of 62.4 Mb and zero gap content, with BUSCO completeness of 99.4%. Genome annotation predicted 23,459 protein-coding genes with annotation BUSCO completeness of 95.0%, and 84.1% of proteins were classified as consistent with the Panthera lineage by OMArk. Repetitive elements occupy 34.01% of the assembly, with retroelements dominating and L1/CIN4 LINEs (15.44%) and SINEs (9.61%) representing the two largest subclasses. Comparative simple sequence repeat (SSR) analysis across six Panthera genomes confirmed a conserved repeat motif architecture, with no lineage-specific expansions detected in P. p. nimr. This nuclear genome complements the mitochondrial reference and provides a foundational resource for future studies on genetic diversity, demographic history, inbreeding load, and conservation planning for the Arabian leopard and other Panthera lineages. Full article

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

Sinotaia angularis is a freshwater viviparid snail with limited genomic resources. Here, we report a chromosome-level reference genome generated using PacBio HiFi sequencing and Hi-C scaffolding, with mitochondrial marker -based screening (16S rRNA and COI (cox1)) and phylogenetic analysis supporting the taxonomic assignment. A total of 74.08 Gb of HiFi reads were obtained, providing approximately 65.7-fold genome coverage. The final assembly spans 1.127 Gb, with a scaffold N50 of 141.87 Mb and a GC content of 34.47%. Hi-C scaffolding anchored 978.89 Mb (86.85% of the assembly) onto eight chromosome-level scaffolds. BUSCO analysis using the mollusca_odb10 dataset recovered 86.9% complete orthologs from the genome assembly. Repeat annotation identified 378.75 Mb of repetitive sequences (33.60% of the genome), with unclassified repeats and LTR elements as the dominant components. Gene annotation predicted 22,232 protein-coding genes, 209 tRNAs, 72 rRNAs, 88 snRNAs, and 10 snoRNAs. Functional annotation assigned database support to 155,611 predicted proteins or isoforms, corresponding to 98% of the total protein set. CAZy annotation identified 5371 carbohydrate-active enzyme entries, suggesting broad carbohydrate-processing potential. This genome provides a reference resource for comparative genomics, chromosome evolution, repeat dynamics, gene-family evolution, and freshwater adaptation studies in Viviparidae. Full article

Mitochondrial genomes are widely used in insect taxonomy and phylogenetics, but their signals may conflict with morphology and nuclear genomic evidence because the mitochondrial genome represents a single maternally inherited locus. Here, we assembled complete mitochondrial genomes of four pygmy grasshoppers, Zhengitettix transpicula, Formosatettix sp., Gibbotettix parvipulvillus, and Bolivaritettix sp., using PacBio HiFi reads. The four mitogenomes ranged from 15,152 to 17,976 bp and contained the typical 37 mitochondrial genes. Mitochondrial phylogenies inferred by maximum likelihood and Bayesian methods were topologically identical and recovered several well-supported tetrigid relationships, including a close relationship between Formosatettix sp. and Bolivaritettix sp. However, Z. transpicula was unexpectedly placed near Macromotettixoides rather than close to other Zhengitettix representatives. In contrast, a morphology-based tree recovered Z. transpicula with Z. triangularis, and comparison with a published nuclear single-copy ortholog tree based on 1962 loci supported a non-mitochondrial placement of Zhengitettix inconsistent with the anomalous mitochondrial position of Z. transpicula. Independent assembly from the original HiFi reads, read-depth inspection, protein-coding gene checks, and nuclear-genome screening for NUMT-like sequences supported the authenticity of the assembled Z. transpicula mitogenome. These results document mito–nuclear and cyto-morphological discordance in Tetrigidae and highlight the need for integrative interpretation of mitochondrial phylogenies in taxonomically complex insect groups. Full article

Neolissochilus heterostomus, a cyprinid fish endemic to Yunnan Province, China, is highly valued for both ornamental and edible purposes, yet its wild populations are currently declining and classified as endangered. In this study, we present a chromosome-level genome assembly of N. heterostomus, utilizing the PacBio HiFi and Hi-C strategies. The assembled genome spans 1793.99 Mb and is anchored to 50 chromosomes, comprising a total of 50,203 genes. Genomic features and chromosomal karyotype data recorded in the present study are consistent with an allotetraploid origin for N. heterostomus. Comparative genomics shows that N. heterostomus shares a close phylogenetic relationship with another allotetraploid fish, the common carp Cyprinus carpio. In total, 4687 expanded and 1365 contracted gene families were identified in N. heterostomus. Further enrichment analyses indicated an overrepresentation of metabolism-related pathways among the expanded and positively selected gene families, whereas the contracted gene families were enriched in reproduction- and embryonic development-related pathways. Reproductive observations further indicate that N. heterostomus produces fewer eggs than other cyprinid species characterized by relatively long embryonic development periods (106.1 h; accumulated temperature: 2260.6 °C·h), including common carp, goldfish (Carassius auratus), grass carp (Ctenopharyngodon idella), pond loach (Misgurnus anguillicaudatus), and blunt snout bream (Megalobrama amblycephala). These findings suggest a potential association between metabolism-related genomic features and reproductive traits, although functional validation remains necessary. Overall, this study may offer insights into the polyploidization, metabolic, and reproductive traits of N. heterostomus, thereby providing genomic and biological resources that may support future studies relevant to the conservation and management of this endangered species. Full article

Lumpy Skin Disease (LSD) is an economically significant viral disease of cattle, widely prevalent across Africa, particularly in sub-Saharan regions. In 2024, Tunisia reported its first outbreak. Understanding the genetic characteristics of lumpy skin disease virus (LSDV) and related poxviruses is critical for surveillance and control. Twenty-nine samples from 26 suspected cases were screened for LSDV using qPCR, followed by a High-Resolution Multiplex Melting (HRM) assay. Three representative samples, two LSDV-positive and one bovine papular stomatitis virus (BPSV)-positive, were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) HiFi long-read technology. Phylogenetic analyses of the LSDV-marker gene RPO30 and complete genomes were performed alongside SNP and InDel profiling. The Tunisian LSDV isolates clustered with Clade 1.2.2 field strains and were 100% identical to each other and to the Italian isolate LSDV_Italy_Sardinia_2025, sharing 99.99% nucleotide identity with LSDV_V281_Nigeria. Although only two LSDV isolates were sequenced which showed no genetic differences, these findings suggest genomic stability within Clade 1.2.2. The Tunisian BPSV isolate showed high similarity (98.15–98.59%) to strains reported in Germany and Switzerland. This study presents the first genetic characterization of LSDV and BPSV in Tunisia, highlighting the importance of accurate differential diagnosis among poxviruses and continuous genomic surveillance to inform control strategies. Full article

Background: Mitochondrial genomes provide valuable information on evolutionary relationships among organisms and on the selective pressures acting on energy metabolism, increasing their relevance in ecological and environmental genomics studies. Haemulon plumierii is a reef-associated fish distributed throughout the Gulf of Mexico and Caribbean Sea and has been proposed as a bioindicator species within the Mesoamerican Reef System. Methods: In this study, we present a high-quality mitochondrial genome of H. plumierii from the southeastern coast of Mexico generated using PacBio HiFi long-read sequencing. Results: The circular mitogenome is 16,823 bp long and contains the complete set of 37 canonical mitochondrial genes, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region (D-loop). The gene order, strand orientation, and tRNA secondary structures were consistent with the conserved vertebrate mitochondrial architecture. Comparative analyses with closely related haemulid species revealed conserved nucleotide composition patterns, negative GC skew values, strong AT enrichment within the D-loop, and highly conserved mitochondrial synteny. Phylogenetic reconstruction based on complete mitochondrial genomes placed H. plumierii firmly within the Haemulon clade. Selective pressure analyses revealed pervasive purifying selection acting on mitochondrial protein-coding genes, supported by low dN/dS ratios, high amino acid identity, constrained nucleotide diversity in cytochrome oxidase genes, and conserved codon usage patterns shaped primarily by AT-driven mutational bias. Pairwise genetic distance analyses further supported moderate interspecific divergence within Caribbean Haemulon species. Conclusions: Overall, the mitogenomic resource generated here provides an important evolutionary and functional framework for future phylogenetic, ecological, and environmental genomics studies in Caribbean reef fishes. Full article

Methylomics has emerged as a central framework for understanding gene regulation in development and disease, yet the rapid expansion of profiling technologies, computational integration methods, and clinical applications has outpaced comprehensive synthesis. This review addresses that gap by systematically examining current advances across the full methylomics pipeline, from data generation to clinical translation. We draw on evidence from large-scale consortium datasets and benchmarking studies of multi-omics integration methods including MOFA, DIABLO, and deep learning architectures, single-cell and spatial methylomic technologies, long-read sequencing platforms (Oxford Nanopore, PacBio HiFi), and cell-free DNA (cfDNA) liquid biopsy approaches. The review further surveys methylation dysregulation across major disease domains, including cancer, cardiovascular disease, neurological disorders, and autoimmune conditions. Integrating methylomic data with transcriptomic and chromatin accessibility layers, particularly in spatial and single-cell contexts, substantially improves the resolution of disease-associated regulatory mechanisms. cfDNA methylation profiling emerges as a cross-disease, non-invasive monitoring platform with broad diagnostic potential, supported by machine learning-based deconvolution. We conclude that while technological barriers are diminishing, standardization of analytical workflows, population diversity in reference datasets, and regulatory alignment remain the principal challenges for translating methylomics advances into broadly accessible precision medicine. Full article

Agricultural pests can rapidly adapt to chemical pressures, and expression-based surveys of chemosensory genes may not fully capture the associated genomic variation. We hypothesized that the molecular profiles of chemosensory and detoxification genes in the mulberry thrips Pseudodendrothrips mori Niwa (Thysanoptera: Thripidae) are associated with local genomic variability and methylation context alongside transcript abundance. To explore this, we integrated PacBio HiFi-derived single-nucleotide polymorphisms (SNPs), structural variants (SVs), DNA methylation, and RNA-seq data on a chromosome-level reference genome. We analyzed 179 focal genes from six families, applying a consensus prioritization framework—based on weighted percentiles of feature values, principal component distances, and anomaly-detection scores—to rank the candidates. The integrated priority score correlated positively with SNP (r = 0.603) and SV burden (r = 0.632) and negatively with local methylation (r = −0.524), whereas its correlation with expression was weaker (r = 0.427). Three OBPs—PSMOgene01223, PSMOgene012530, and PSMOgene012982—emerged among the highest-priority candidates, exhibiting favorable in silico docking scores (−5.038 to −6.792 kcal/mol) with (Z)-octadec-11-enyl acetate and a long-chain oxygenated acetate. These findings indicate potential linkages between multi-omics plasticity and chemosensory gene variation. Furthermore, these computationally prioritized OBPs suggest potential targets for exploring semiochemical-based management tools. Full article

Quercus oxyphylla (E. H. Wilson) Hand.-Mazz. is a threatened evergreen subalpine tree species with fragmented habitats native to China. Here, we present a de novo chromosome-level genome assembly of this oak species by integrating PacBio long-read high-fidelity (HiFi) sequencing and Hi-C mapping technologies. The assembled genome size of Q. oxyphylla in this study is 824.15 megabases (Mb) in length with 12 putative chromosomes. Genome annotation of this oak species identified 514.09 Mb of repeat sequences, 53,730 protein-coding genes and 1048 non-coding RNA sequences. Genomic analyses of whole-genome duplication (WGD) and long terminal repeat retrotransposon (LTR-RT) insertion events in Q. oxyphylla revealed no species-specific WGD and recent accumulation of LTR-RTs in the genome within the last seven million years. A phylogenomic analysis with eight oak representatives confirmed the framework phylogeny of genus Quercus and indicated that Q. oxyphylla possibly split with the ancestor of Cerris oaks about 20.4 million years ago. We identified 2074 expanded and 903 contracted gene families across the genome assembly of Q. oxyphylla, while the significantly expanded gene families had notable disease resistance-related genes that were mainly enriched in plant–pathogen interaction pathways. The high-quality genome assembly of Q. oxyphylla generated in this study provides a valuable genome resource for the genetic conservation and management of Q. oxyphylla, and may facilitate our understanding of genome evolution and species adaptation of the oak lineage. Full article