Science unlocked: publication picks from April 2025

In this monthly series, we share a selection of recent publications in which Oxford Nanopore sequencing was used to unlock novel insights. Spanning from direct RNA modification detection, to near-complete genome assembly, to mRNA vaccine development, these studies showcase the advances in scientific research made possible by Oxford Nanopore sequencing.

Featured in this edition:

1. Tackling a cereal killer

2. Near-complete telomere-to-telomere assembly

3. A new chapter in RNA biology

4. The key to mRNA vaccine success

5. Revealing complex genomic events in cancer

Plant

1. A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity (BMC Genomics)

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), threatens global food security. Using Oxford Nanopore sequencing, researchers rapidly genotyped field samples in under 48 hours, detecting lineage and fungicide resistance. This approach enables full-gene coverage, variant phasing, and is deployable in low-resource settings — supporting faster, more informed disease control strategies against this ‘cereal killer’.

Key points:

• Savva et al. introduce the Pgt MARPLE diagnostics platform: a portable, real-time genotyping tool designed to close the wheat stem rust surveillance gap

• 165 Pgt isolates were collected from 25 countries across the world

• Using Oxford Nanopore sequencing of a targeted panel of 276 genes and a standard laptop, MARPLE delivered lineage typing and fungicide resistance profiling within 48 hours of leaf sample collection

• The method has already been successfully deployed in Kenya and Ethiopia, placing powerful genomic tools in the hands of local teams and enabling faster, more informed responses to emerging outbreaks

Figure: Primers were successfully designed for 276 highly polymorphic Pgt genes for use in the MARPLE diagnostics platform. These genes were sufficient to accurately reconstruct the phylogeny generated using the complete set of 1,611 polymorphic Pgt genes. Redistributed from Savva et al. 2025 under Creative Commons Attribution License CC BY 4.0.

Bioinformatics / platform capabilities

2. Efficient near telomere-to-telomere assembly of nanopore simplex reads (bioRxiv)

Cheng and Qu et al. introduce hifiasm (ONT), the first algorithm to achieve near telomere-to-telomere (T2T) genome assemblies using standard Oxford Nanopore reads obtained with the Ligation Sequencing Kit — no ultra-long reads required. Providing greater contiguity at a lower cost and computational demand, this algorithm outperforms traditional methods and could make high-quality assemblies accessible for a broad range of applications, from clinical research to biodiversity genomics.

Key points:

• Hifiasm (ONT) performs efficient error correction by using phasing information to distinguish true variants from errors

• The algorithm assembled highly accurate and contiguous genomes across multiple human and non-human samples

• Compared with PacBio HiFi assemblies, Oxford Nanopore assemblies exhibited substantially higher contiguity and comparable quality, even within repetitive regions

• Hifiasm (ONT) outperformed Verkko+HERRO in T2T count and contiguity while running an order of magnitude faster and requiring less computational resource

• It demonstrated the ability to resolve complex, medically relevant loci such as the highly homologous SMN1 and SMN2 genes that are linked to spinal muscular atrophy

• Hifiasm (ONT) enables cost-effective, scalable genome assembly without the need for complex laboratory protocols or high computational overhead

Read our news summary or catch the talk by lead algorithm designer Haoyu Cheng at London Calling 2025 to find out more

3. The detection, function, and therapeutic potential of RNA 2'-O-methylation (The Innovation Life)

The RNA modification 2'-O-methylation (Nm) is an essential RNA modification found across nearly all types of RNAs. This review compares Nm detection methods, and examines its biological roles in health and disease. Researchers have recently used Oxford Nanopore direct RNA sequencing and the NanoNm machine learning tool to map thousands of Nm sites at single-base resolution. They found that Nm has regulatory and structural roles, with implications for cancer, neurodegeneration, and viral immune evasion — highlighting its potential as a biomarker and therapeutic target in the future.

Key points:

• Oxford Nanopore technology enabled amplification-free, full-length RNA sequencing and quantitative Nm detection with single-nucleotide precision, overcoming the major limitations of short-read and chemical-based methods

• NanoNm enables de novo, single-base resolution of Nm from Oxford Nanopore direct RNA sequencing data

• Thousands of Nm sites have been identified in human mRNA and rRNA

• Stoichiometric analysis suggests Nm plays a regulatory role in mRNA and a structural role in rRNA

• Nm is enriched near stop codons and linked to mRNA stability, shortened 3'-UTRs, and increased gene expression

• Fibrillarin overexpression increases Nm on cancer-related transcripts, linking Nm to disease-relevant gene regulation

• Studying Nm could reveal novel diagnostic markers and therapeutic strategies for a wide range of diseases in the future

Find out more about direct RNA sequencing in our workflow overview

Biopharma

4. Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines (Nature)

Despite their widespread use, intracellular studies of mRNA vaccines have been limited. Using direct RNA Oxford Nanopore sequencing, researchers uncovered a novel mechanism enhancing mRNA vaccine performance: re-adenylation by TENT5A. This enzyme extends mRNA poly-A tails to boost mRNA stability and antigen production. This study showcases how nanopore sequencing enables real-time, single-molecule insights into mRNA metabolism — offering a strategy to improve future RNA-based therapeutics.

Key points:

• Krawczyk et al. used Oxford Nanopore direct RNA sequencing to study the poly-A tails of individual therapeutic mRNA molecules

• The results showed that therapeutic mRNAs can have their poly-A tails extended within cells. This increases their stability and production of coded antigens, potentially explaining the efficacy of existing mRNA vaccines

• By exploring the immune response to mRNA vaccination, they identified the biological mechanism for the poly-A extension — re-adenylation by TENT5A

• The findings reveal a principal that could be harnessed to improve the efficacy of mRNA therapeutics in the future

Figure: Overview of the enhanced direct RNA sequencing approach for studying mRNA therapeutics. RNA molecules passing through the pores from the 3′ end alter the electric current readout, which are then basecalled and used to calculate the poly-A length or to detect the presence of a terminal mΨCmΨAG pentamer. Redistributed from Krawczyk et al. 2025 under Creative Commons Attribution License CC BY 4.0.

Cancer

5. Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing (Nature Biotechnology)

Keskus et al. developed Severus, a breakpoint graph-based algorithm for somatic structural variant (SV) calling from Oxford Nanopore and PacBio data. Severus outperformed other long- and short-read SV callers and identified clinically relevant rearrangements in tumour samples that were missed by standard genomic panels. This research demonstrates the value of accurate SV calling for precision oncology and provides new tools and data to advance cancer genomics in the future.

Key points:

• Severus works with tumour-only and matched normal samples, produces haplotype-specific SV calling, characterises complex SV patterns, and supports unbalanced cancer karyotypes

• Severus identified clinically relevant, cryptic SVs in paediatric leukaemia and lymphoma research samples that were missed by routine clinical tests

• Using a phased breakpoint graph, Severus reconstructed complex genomic events such as chromoplexy

• This algorithm outperforms existing SV detection methods, which struggle with the complex rearrangements and heterogeneity associated with tumour SV calling

Inspired? Apply Oxford Nanopore sequencing to your own research questions and you'll never see sequencing the same way again. Explore the nanopore sequencing solution.

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