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PubMed2026

Nanopore-based epigenomic profiling reveals the absence of widespread CpG methylation in the African swine fever virus genome.

DNA methylation is a critical epigenetic mechanism implicated in regulating replication and transcription in DNA viruses. However, the epigenetic landscape of African swine fever virus (ASFV), a large double-stranded DNA virus infecting pigs, remains controversial. Here, we systematically profiled the DNA methylome of the first ASFV strain isolated in Hong Kong (HK_NT_202103) using Oxford Nanopore Technologies (ONT) R10.4.1 sequencing. We employed a paired design: native whole-genome sequencing (WGS) against a methylation-free whole-genome amplification (WGA) control. Using conservative thresholds, we found no evidence of 5-methylcytosine (5mC), especially typical CpG methylation, across the viral genome. Importantly, clear CpG methylation signals were successfully detected in the host genome from WGS data, confirming the functionality of the workflow to detect 5mC at CG sites. While widespread 5mC seems absent, a small number of putative N6-methyladenine (6mA) loci were identified. A specific 6mA candidate exhibited raw ionic current disruptions and gene-level intersection with another ASFV isolate (CAS19-01/2019), although it lacked single-base consensus across different methylation callers or between the two isolates. Although our biological findings are restricted to a single isolate under specific experimental conditions, this study introduces a novel, highly rigorous ONT framework for viral epigenomics research. Furthermore, the absence of ASFV CpG methylation indicates that host CpG-depletion remains a viable strategy for viral metagenomic enrichment. Ultimately, our work offers a critical methodological baseline for ASFV surveillance and highlights the necessity of targeted experimental validation for rare viral modifications.

African Swine Fever Virus↗

PubMed2026

New insights on Plasmodium gene expression from direct RNA sequencing.

Oxford Nanopore Technology (ONT) direct RNA sequencing enables the sequencing of native RNA molecules without cDNA conversion. The long-read approach captures full-length reads spanning entire genes and has transformed the study of gene expression in Plasmodium parasites by enabling analysis of untranslated regions, isoforms, and alternative splicing. In addition, ONT provides unique insights into non-coding RNAs, RNA modifications, and polyadenylated tail dynamics, which are expanding our understanding of post-transcriptional regulation in Plasmodium, including processes beyond translational repression in gametocytes and sporozoites. Here, we discuss the past and future applications of direct RNA sequencing in Plasmodium research and highlight its advantages, limitations, and future prospects.

Oxford Nanopore Technology↗

PubMed2024

Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows.

BACKGROUND: Drug-resistant tuberculosis remains a major obstacle in ending the global tuberculosis epidemic. Deployment of molecular tools for comprehensive drug resistance profiling is imperative for successful detection and characterisation of tuberculosis drug resistance. We aimed to assess the diagnostic accuracy of a new class of molecular diagnostics for drug-resistant tuberculosis. METHODS: We conducted a prospective, cross-sectional, multicentre clinical evaluation of the performance of two targeted next-generation sequencing (tNGS) assays for drug-resistant tuberculosis at reference laboratories in three countries (Georgia, India, and South Africa) to assess diagnostic accuracy and index test failure rates. Eligible participants were aged 18 years or older, with molecularly confirmed pulmonary tuberculosis, and at risk for rifampicin-resistant tuberculosis. Sensitivity and specificity for both tNGS index tests (GenoScreen Deeplex Myc-TB and Oxford Nanopore Technologies [ONT] Tuberculosis Drug Resistance Test) were calculated for rifampicin, isoniazid, fluoroquinolones (moxifloxacin, levofloxacin), second line-injectables (amikacin, kanamycin, capreomycin), pyrazinamide, bedaquiline, linezolid, clofazimine, ethambutol, and streptomycin against a composite reference standard of phenotypic drug susceptibility testing and whole-genome sequencing. FINDINGS: Between April 1, 2021, and June 30, 2022, 832 individuals were invited to participate in the study, of whom 720 were included in the final analysis (212, 376, and 132 participants in Georgia, India, and South Africa, respectively). Of 720 clinical sediment samples evaluated, 658 (91%) and 684 (95%) produced complete or partial results on the GenoScreen and ONT tNGS workflows, respectively, with 593 (96%) and 603 (98%) of 616 smear-positive samples producing tNGS sequence data. Both workflows had sensitivities and specificities of more than 95% for rifampicin and isoniazid, and high accuracy for fluoroquinolones (sensitivity approximately ≥94%) and second line-injectables (sensitivity 80%) compared with the composite reference standard. Importantly, these assays also detected mutations associated with resistance to critical new and repurposed drugs (bedaquiline, linezolid) not currently detectable by any other WHO-recommended rapid diagnostics on the market. We note that the current format of assays have low sensitivity (≤50%) for linezolid and more work on mutations associated with drug resistance is needed. INTERPRETATION: This multicentre evaluation demonstrates that culture-free tNGS can provide accurate sequencing results for detection and characterisation of drug resistance from Mycobacterium tuberculosis clinical sediment samples for timely, comprehensive profiling of drug-resistant tuberculosis. FUNDING: Unitaid.

Humans↗

PubMed2025

Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis.

MOTIVATION: Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in "k-mer models." In cases where official models are lacking or unsuitable for specific sequencing conditions, tailored k-mer models are crucial to ensure precise signal-to-sequence alignment, analysis and interpretation. The process of transforming raw signal data into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing. RESULTS: In this study, we leverage the move table produced by ONT's basecalling software to create a lightweight de novo k-mer model for RNA004 chemistry. We demonstrate the validity of our custom k-mer model by using it to guide signal-to-sequence alignment analysis, achieving high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models another analysis, such as detection of m6A RNA modifications. We provide our method, termed Poregen, as a generalizable approach for creation of custom, de novo k-mer models for nanopore signal data analysis. AVAILABILITY AND IMPLEMENTATION: Poregen is an open source package under an MIT license: https://github.com/hiruna72/poregen.

Nanopore Sequencing↗

PubMed2026

NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis.

SUMMARY: Long-read RNA sequencing technologies, including Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enable direct characterization of full-length transcripts and transcriptome complexity. However, analysis of long-read RNA-seq data remains fragmented across multiple tools, limiting the ability to obtain a unified view of transcript structure, expression, and regulatory variation in long-read transcriptomes. We present NextLongIso, a scalable and reproducible Nextflow pipeline that enables coordinated analysis of multiple layers of transcript regulation. Rather than focusing solely on transcript reconstruction, NextLongIso integrates transcript discovery with downstream regulatory analyses to jointly characterize alternative splicing, isoform switching, transcript boundary dynamics (including alternative promoters and polyadenylation), and transposable element-associated transcription from both PacBio and ONT datasets. By eliminating complex cross-tool data harmonization, this unified framework facilitates the transition from transcript identification to functional interpretation of transcriptomic variation. AVAILABILITY AND IMPLEMENTATION: NextLongIso is implemented in Nextflow and is freely available at github: https://github.com/YidanSunResearchLab/nf-LongIso.git and Zenodo: https://doi.org/10.5281/zenodo.21049837.

Software↗

PubMed2025

IBDV-SSA, a novel molecular approach for the recovery of infectious bursal disease virus whole genomes from FTA cards.

Infectious bursal disease (IBD), a highly contagious viral disease in young chickens, poses significant economic losses due to high mortality and immunosuppression. While IBD virus (IBDV) virulence is influenced by multiple genes, whole-genome sequencing (WGS) of IBDV is crucial for defining the strain pathotype and clinical profile. Flinders Technology Associates (FTA) cards are convenient for field sample collection, but their filter paper matrix can hinder nucleic acid recovery, impacting sequencing efficiency. This study evaluated two enrichment strategies, single primer amplification (SPA) and IBDV segment-specific amplification (SSA), coupled with short-read (Illumina) and long-read (Oxford Nanopore Technologies, ONT) sequencing platforms, to optimize IBDV whole-genome recovery from FTA cards. Illumina sequencing produced comparable raw read counts for both methods, yet IBDV-SSA samples achieved significantly higher genome mapping rates (76%) than IBDV-SPA (12%). Genome coverage analysis revealed that IBDV-SSA provided uniform read distribution across both genomic segments, ensuring complete coverage, while IBDV-SPA exhibited significant bias, with most reads mapping to segment B, and limited coverage of segment A. Importantly, IBDV-SSA also proved compatible with ONT long-read sequencing, providing complete genome coverage. Notably, IBDV-SSA coupled with short-read sequencing successfully characterized coinfections in two samples. This optimized approach using IBDV-SSA enables efficient and comprehensive WGS of IBDV from FTA cards, facilitating strain characterization, virulence prediction, and epidemiological investigations.IMPORTANCEThis research tackles a significant problem for poultry farmers: a virus called infectious bursal disease virus (IBDV) that harms young chickens, causing high death rates and economic losses. To fight it effectively, scientists need to analyze its complete genetic makeup. Traditionally, collecting and preserving IBDV field samples was challenging. Flinders Technology Associates (FTA) cards have simplified this process, but getting usable genetic material from them has been difficult. This study introduces a new genome enrichment method, IBDV segment-specific amplification (IBDV-SSA), which successfully allows for IBDV complete genome recovery from FTA cards. By using this improved approach, scientists can accurately identify virus strains, assess how harmful they are, and monitor their spread. This, in turn, helps to improve vaccines and protect flocks. IBDV-SSA is a powerful tool for outbreak surveillance, supporting the poultry industry and ensuring a stable food supply.

Infectious bursal disease virus↗

PubMed2025

Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement.

INTRODUCTION: Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is essential for improving treatment outcomes. Phenotypic drug susceptibility testing (pDST) is comprehensive but slow, while rapid molecular assays provide resistance information for a limited number of drugs. Targeted next-generation sequencing (tNGS) offers the potential for broad and rapid resistance detection, but its integration into diagnostic algorithms has been hindered by uncertainty about its placement within existing workflows. METHODS: This study evaluated the extent to which two tNGS solutions-Deeplex Myc-TB (GenoScreen) and TB Drug Resistance Test (Oxford Nanopore Technologies, ONT)-provided interpretable drug resistance results that could inform regimen design, in comparison to other WHO-recommended molecular assays and pDST. Data were collected from three high-burden DR-TB settings under the Seq&Treat study. Sequencing success rates and drug resistance detection were analysed based on: (1) the initial Xpert MTB/RIF result (very low, low, medium, high), (2) resistance results for drugs in WHO-recommended regimens and (3) performance relative to other WHO-endorsed assays. The potential impact of different algorithms on the estimates was also considered. Key factors influencing successful tNGS adoption within diagnostic pathways were identified, leveraging insights from the Seq&Treat diagnostic accuracy study. RESULTS: Sequencing success rates were 88.5% (GenoScreen) and 93.1% (ONT) across 763 samples. While tNGS provided complete resistance data for 73%-86% of drugs in recommended regimens, pDST achieved 92%-93%. Both tNGS solutions matched or exceeded the sensitivity of WHO-recommended molecular assays. CONCLUSIONS: This study highlights the critical role of tNGS as a centralised tool for comprehensive drug resistance testing to inform DR-TB treatment decisions following initial screening assays. By complementing existing molecular tests with tNGS, diagnostic workflows can be optimised to ensure timely and comprehensive resistance detection. These findings support policy updates to integrate tNGS into global TB diagnostic algorithms. TRIAL REGISTRATION NUMBER: NCT04239326.

Humans↗

PubMed2026

Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.

BACKGROUND: Short tandem repeats (STRs) are repetitive DNA sequences with 1–6 nucleotide repeat units, exhibiting high polymorphism due to varying repeat counts. STRs are more variable than SNPs and can cause genetic disorders. With population-scale cattle whole-genome sequencing data available, whole-genome STR identification has attracted new interest, but challenges remain due to the lack of standardized methods, sequencing data limitations, and the diversity of STR-calling tools. This study compared six STR-calling tools: HipSTR, GangSTR, and ExpansionHunter for short-read data, and Straglr, RepeatHMM, and LongTR for Oxford Nanopore (ONT) long-read data—using sequences from five Holstein cattle (two parent–offspring trios with a shared sire). This is the first cattle study to evaluate short- and long-read STR callers using both data types from the same animals. RESULTS: In short-read data, ExpansionHunter identified the highest number of polymorphic STRs (pSTRs) (327,690), followed by HipSTR (205,900) and GangSTR (110,680), with 93,023 loci detected by all three tools. In long-read data, LongTR detected 470,250 pSTRs, RepeatHMM 224,185, and Straglr 90,275, with only 33,253 loci shared among them. Mendelian consistency of STR genotypes in the trio offspring was high (> 0.8) for all short-read tools, with HipSTR and GangSTR highest at 0.98. LongTR was the only long-read tool with high consistency (0.88). Short-read tools also showed higher concordance in STR genotypes among themselves than was observed among long-read tools. However, long-read tools had a clear advantage in detecting large STRs. Relative to computational efficiency, HipSTR and GangSTR (short-reads), and LongTR (long-reads) required less memory and shorter runtimes than the other tools. CONCLUSIONS: Tool selection is critical for accurate whole-genome STR identification in cattle. For short-read data, HipSTR showed relatively high Mendelian consistency and concordance compared to the other tools, while ExpansionHunter was able to detect longer STRs but with lower Mendelian consistency. For long-read data, LongTR demonstrated higher consistency and computational efficiency relative to the other tools. Based on these results, HipSTR and LongTR are suggested as preferred options for short-read and ONT long-read datasets, respectively, in cattle STR analysis. These recommendations are based on the metrics observed in this study, and confirmatory analyses across additional breeds, larger sample sizes, and validated truth sets are encouraged.

Animals↗

PubMed2026

Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing.

BACKGROUND: CAG repeat expansions in ATXN2 are implicated as risk factors for several neurological diseases, including spinocerebellar ataxia type 2 (SCA2) when >=33 CAG repeats are present, and amyotrophic lateral sclerosis (ALS) when 27-33 CAG repeats are present. However, how haplotypes around the repeats and CAA interruptions within the repeats are associated with disease phenotypes remains poorly understood. Previous studies on haplotypes around ATXN2 were limited to SNPs very close to the repeats (<5kb) or were based on statistical inference only. METHODS: Here, we used long-read sequencing on the Oxford Nanopore Technologies (ONT) platform to simultaneously infer haplotypes around ATXN2, the number of CAG repeats, and the number of CAA interruptions, along with NYGC ALS Consortium NGS dataset. We further sequenced 41 individuals (EUR = 39) with neurological diseases with intermediate repeats by ONT. RESULTS: We found that haplotypes around ATXN2 and the number of interruptions show ethnicity-specific and ALS-specific distribution. Three CAA interruptions are present at low prevalence (~1%) in control populations in multiple ancestry groups, but high prevalence (~55%) in ALS individuals with intermediate repeats. Furthermore, we examined 159 individuals with ALS (~90% European ancestry) with intermediate ATXN2 repeats and found a unique haplotype in ALS individuals with three CAA interruptions, which can be tagged by an SNV, rs148019457. We also validated that the rs148019457-G allele is only present in haplotypes with three CAA interruptions. CONCLUSIONS: In summary, our study shows that 3 CAA interruptions are rarely seen in healthy controls but are common in those with expanded ATXN2 CAG repeats who have neurological disorders, and that rs148019457 tags a specific haplotype with 3 CAA interruptions within expanded ATXN2 CAG repeats in individuals of European ancestry. These results have implications for the development of precision genomic medicine for neurological disorders, and the tag SNP may help identify those with interruptions from existing population genotyping data.

ATXN2↗

PubMed1979

Analysis of sudden unexpected death in southern Ontario, with emphasis on myocarditis.

The records of all 2427 autopsies performed at the Brantford (Ont.) General and Paris (Ont.) Willett hospitals from Jan. 1, 1969 to Aug. 15, 1978 were reviewed. Of the 1299 cases of sudden unexpected death investigated by a coroner almost 28% were due to unnatural causes--violence or poisoning. The main cause of natural sudden death was coronary artery disease, which accounted for 43.3% of all the sudden unexpected deaths. In 20 cases the cause of death was thought to be viral myocarditis, and in 9 of the 20 there was serologic evidence of at least previous coxsackievirus disease. Two of the nine cases were of special interest because of the finding of giant-cell myocarditis in one and aortic valve disease in the other. Eleven of the 20 persons were aged 13 to 46 years. These findings support the view that the most serious manifestation of enterovirus infection today is cardiac damage by coxsackieviruses.

Adolescent↗

PubMed2026

Chromosome-level assembly and annotation of the Jaguar (Panthera onca) genome.

OBJECTIVES: The Jaguar (Panthera onca) is a large cat species native to the Americas. Despite being successful predators, jaguar populations have declined due to habitat loss. Genome resources can help in conservation efforts as well as in understanding the interesting biology of these Felids. Beside contiguity, a well annotated reference genome provides contextual information for variants that will benefit the design of appropriate conservation programs. DATA DESCRIPTION: We sequenced material from two individuals using a combination of ONT reads and Illumina PE. The resulting nuclear genome assembly has a larger contig N50 (48.04 Mb) compared with the existing annotated chromosome-level assembly published by the DNA Zoo project. Using public Hi-C data, we obtained an improved chromosome-level assembly of the Jaguar genome (mPanOnc3.5) with larger contigs, 99.85% of the sequence assigned to chromosomes and 25,267 protein coding genes annotated. Overall, this improved assembly provides a better reference to study this threatened species.

Animals↗

PubMed2026

Characterization and genomic analysis of Bacillus halotolerans G3-2: a potential biocontrol agent against apple Alternaria leaf blotch disease.

BACKGROUND: Apple Alternaria leaf blotch (ALB) is a devastating disease threatening the apple industry worldwide. Biocontrol offers an effective and environmentally friendly alternative for disease management. RESULTS: Bacillus strain G3-2 exhibits strong antagonistic activity against Alternaria alternata (a major causal pathogen of ALB). In dual-culture assays, G3-2 inhibited A. alternata by 88.39%; in detached-leaf inoculation assays, it reduced the lesion area by >88%. 16S rRNA sequencing and phylogenetic analysis identified this strain as Bacillus halotolerans. Oxford Nanopore Technology (ONT) sequencing generated a 4.18-Mb complete genome (43.8% G + C) containing 4149 protein-coding genes, 30 rRNAs and 86 tRNAs. CAZy annotation identified 182 genes encoding carbohydrate-active enzymes (CAZymes), including glycoside hydrolases, glycosyltransferase, and carbohydrate esterases, suggesting potential for glycosylated secondary metabolite production. AntiSMASH analysis detected nine biosynthetic gene clusters, including those for surfactin, fengycin, bacillaene and laterocidine. Plate assays confirmed that G3-2 has the ability to produce protease, cellulase and siderophore. Moreover, it exhibits ~70% inhibition against several other phytopathogenic fungi. CONCLUSIONS: These findings demonstrate that G3-2 suppresses A. alternata through antibiosis (lipopeptides and polyketides), nutrient competition (siderophores) and cell-wall degradation (proteases and cellulases). Moreover, our study revealed that it has great potential to be used as a broad-spectrum, environmentally friendly biocontrol agent. © 2026 Society of Chemical Industry.

Alternaria↗

PubMed2027

Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.

This protocol provides a comprehensive, step-by-step workflow for whole-genome sequencing of Chikungunya virus (CHIKV) using an amplicon-based strategy optimized for Oxford Nanopore Technologies (ONT) platforms. The procedure includes detailed instructions for sample handling, viral RNA extraction, quality control, cDNA synthesis, multiplex PCR amplification, library preparation, sequencing, and primary bioinformatic processing. The protocol is designed to maximize reproducibility across laboratories and is suitable for genomic surveillance applications, including outbreak investigation and molecular epidemiology, even when working with low-to-moderate viral loads.

Chikungunya virus↗

PubMed2025

Molecular-based evidence for school transmission of enteroaggregative Escherichia coli among apparently healthy children attending nursery, infant, and primary schools in Madrid (Spain).

UNLABELLED: Information on the epidemiology, transmission dynamics, and public health impact of enteroaggregative Escherichia coli (EAEC) infection in schoolchildren from high-income countries is scarce. This study investigated the occurrence of EAEC infections in apparently healthy children (0-12 years) attending nursery, infant, and primary schools in Spain. High-resolution whole-genome sequencing typing was used to detect and trace back unnoticed episodes of transmission within school settings. An overall EAEC prevalence of 5.1% was observed, with children in the 0-3 age group showing the highest prevalence (24.2%). Besides their gastrointestinal potential, 17% of EAEC isolates revealed an additional urinary/systemic pathogenic potential. Presumptive outbreaks of EAEC infection were identified in two different nursery schools involving the endemic subtypes O126:H27-ST200 (15 children) and O111:H21-ST40 (12 children). Most affected children shared caregivers and common areas including activity, eating, sleeping, and diapering/toileting rooms. Direct person-to-person transmission was highly suspected, although foodborne transmission could not be completely ruled out. Six independent micro-foci of EAEC infections were additionally identified in five different infant and primary schools also involving O126:H27-ST200 (two children) and O111:H21-ST40 (three children), as well as O3:H2-ST10 (three children), O44:H18-ST1380 (two children and two siblings), and ONT:H33-ST34 (four children). No clear information was available on the sources of infection and transmission routes in these settings. CONCLUSION: Apparently healthy Spanish schoolchildren may be carriers and potential spreaders of certain EAEC subtypes with gastrointestinal/extra-intestinal pathogenic potential. While transmission within school settings appears to be the most likely explanation for the EAEC genomic clusters identified, particularly among toddlers, extra-school infections through alternative pathways cannot be entirely ruled out. WHAT IS KNOWN: • EAEC is increasingly considered as an important agent of domestically acquired paediatric diarrhoea in high-income countries. • Endemic EAEC subtypes differ between low- and high-income countries. WHAT IS NEW: • Apparently healthy children in high-income countries may be carriers and potential spreaders of certain EAEC subtypes with gastrointestinal/extra-intestinal pathogenic potential. • Transmission of endemic EAEC subtypes can occur within school settings, particularly during early childhood, without precluding other transmission modes.

Humans↗

PubMed2026

An enhanced multisegment RT-PCR method for influenza A virus sequencing: Improved performance and reduced preparation time over traditional methods.

Influenza A viruses (IAVs) remain a major global health threat, affecting both human and animal populations. Whole-genome sequencing is essential for monitoring viral evolution, zoonotic transmission, and emerging variants. However, conventional RT-PCR methods often result in incomplete gene coverage, amplification biases, and reduced sequencing accuracy, particularly in clinical samples. We developed a robust In-house method for IAV full-genome sequencing using the Oxford Nanopore Technologies (ONT) long-read sequencing platform. This method integrates an in-house multisegment Reverse Transcription PCR (RT-PCR) method with a streamlined 2-pool primer design targeting all eight IAV gene segments. RNA extracted from clinical and stock virus samples was reverse-transcribed and amplified using Superscript IV-based chemistry, followed by magnetic bead purification to ensure high-quality amplicons. Sequencing libraries were prepared with the Native Barcoding Kit 24 (SQK-NBD114.24) and sequenced on R10.4.1 flow cells on the MinION MK1C device. Data analysis using the Iterative Refinement Meta-Assembler (IRMA) confirmed improved read depth, uniform coverage, and complete genome recovery. Compared to conventional methods, our In-House Multisegment 2-Pool (IH-MS2P) RT-PCR method generated higher numbers of matched read counts, minimized chimeric artifacts, and delivered superior genome coverage across human, swine, and avian isolates. This optimized RT-PCR method provides a high-performance, time-efficient, and portable solution for influenza genomics, demonstrating robust applicability even with clinical samples of low RNA yield.

Influenza A virus↗

PubMed2025

A telomere-to-telomere gap-free genome assembly of the endangered humphead wrasse (Cheilinus undulatus).

Humphead wrasse, Cheilinus undulatus, is an endangered fish species with high economic and ecological value as well as natural sex change from female to male, while sexual selection occurs in breeding aggregations. In our present study, we constructed the first gap-free telomere-to-telomere (T2T) genome assembly for humphead wrasse, by integration of PacBio HiFi, ONT Ultra-long and Hi-C sequencing techniques. With 99% of the entire sequences anchored into 24 chromosomes, this haplotypic genome assembly spans approximately 1.25 Gb and presents a complete set of 48 telomeres and 24 centromeres. In terms of correctness (quality value QV: 53.447) and completeness (BUSCO score: 99.3%), this chromosome-scale assembly is indeed of high quality. We predicted 658.03 Mb of repetitive sequences and annotated 26,609 protein-coding genes in the assembled genome. This high-quality T2T genome assembly not only facilitates the genetic conservation of humphead wrasse, but also offers fundamental genomic data for supporting in-depth investigations on functional genomics, genetic diversity, and selective breeding for this economically important teleost.

Animals↗

PubMed2025

Chromosomal level genome assembly of medicinal plant Chrysosplenium macrophyllum.

Chrysosplenium macrophyllum Oliv., a perennial herb native to China, is widely used in traditional medicine for its notable therapeutic properties. However, the absence of a reference genome has constrained its full potential for research and application. This study presents the first chromosome-level de novo genome assembly of C. macrophyllum, constructed by integrating long reads from Oxford Nanopore Technologies (ONT), short reads from BGI, and Hi-C data. The final assembly spans 2.55 Gb, with a scaffold N50 of 93.38 Mb, and 83.70% of the genome has been assigned to 22 chromosomes. The mapping rate of the BGI short reads to the genome is approximately 97.94%, and BUSCO analysis reveals that 97.94% of the predicted genes are complete. A total of 62,921 protein-coding genes were predicted, with functional annotations for 93.67% of them. This chromosome-level genome assembly represents an important resource for expanding our understanding of Chrysosplenium species and supports future genomic studies and applications.

Genome, Plant↗

PubMed2025

A telomere-to-telomere reference genome assembly of the red silk cotton tree (Bombax ceiba).

Bombax ceiba, an important ornamental tree and potential fiber resource in the textile industry, is widely distributed in tropical and subtropical regions. In this study, we assembled a nearly gap-free telomere-to-telomere (T2T) genome of B. ceiba using Illumina, PacBio High-fidelity (HiFi), ONT ultra-long, and Hi-C sequencing technologies. The genome spanned approximately 807.89 Mb, with a scaffold N50 of 16.58 Mb, and 754.68 Mb (93.41%) of genomic sequences were anchored onto 48 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis revealed a completeness of 99.40%, identifying 1,378 single-copy and 213 duplicated genes out of 1,614. The genome contained 67.72% (547.11 Mb) repeat regions, with 39,708 predicted protein-coding genes. Collectively, our study provides valuable genomic data for investigating the evolutionary history of the Malvaceae family.

Genome, Plant↗