Genomics

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years

1. Megan A Phillips
2. Robert A Petit
3. Daniel B Weissman
4. Timothy D Read

• Curated by eLife

  eLife Assessment

  Using genome databases, the authors performed solid bioinformatic analyses to trace the genomic history of the clinically relevant Staphylococcus aureus tetracycline resistance plasmid pT181 over the last seven decades. They discovered that this element has transitioned from a multicopy plasmid to a chromosomally integrated element, and the work represents a valuable demonstration of the use of publicly available data to investigate plasmid biology and inform clinical epidemiology. This work will appeal to researchers interested in staphylococcal evolution, plasmid biology, antimicrobial resistance and bacterial genome structure.

Reviewed by eLife

Evolutionary remodeling of non-canonical ORF translation in mammals

1. Yue Chang
2. Tianyu Lei
3. Feng Zhou
4. Jiawen Jiang
5. Yu Huang
6. Ziyang Zhu
7. Hong Zhang

• Curated by eLife

  eLife Assessment

  This valuable study provides a systematically curated atlas of non-canonical open reading frames translated across normal human and mouse tissues by uniformly integrating nearly 400 ribosome-profiling datasets with independent mass-spectrometry evidence for ncORF-encoded peptides. The convincing analyses connect ncORF evolutionary age and coding constraint with translation level, tissue distribution, and co-translation with canonical coding sequences, offering a broad comparative view of how non-canonical translation changes over mammalian evolution. Although the functions of most ncORF-encoded peptides remain unknown, the scale of their detection across tissues, together with their proteomic and evolutionary signatures, suggests that a substantial subset may have biological functions.

Reviewed by eLife, Arcadia Science

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

1. Kuan-Hao Chao
2. Majed Mohamed Magzoub
3. Emily H. Stoops
4. Sean Hackett
5. Johannes Linder
6. David R. Kelley

• Curated by eLife

  eLife Assessment

  This important study shows that self-supervised pretraining on related fungal genomes can substantially improve sequence-to-expression prediction in budding yeast. The evidence for the main conclusion is convincing, with careful comparisons to models trained from random initialization and clear gains on held-out expression data. The broader claims about the optimal evolutionary scope and transfer of regulatory grammar are less fully supported.

Reviewed by eLife

A new diagnostic modality for bovine tuberculosis: accurate and robust classification of infected cattle using transcriptomics and machine learning

1. John F O’Grady
2. Adriana Ivich
3. Gillian P McHugo
4. Adnan Khan
5. Thomas J Hall
6. Sarah L Faherty O’Donnell
7. Carolina N Correia
8. John A Browne
9. Valentina Riggio
10. James GD Prendergast
11. Emily L Clark
12. Hubert Pausch
13. Kieran G Meade
14. Isobel C Gormley
15. Eamonn Gormley
16. Stephen V Gordon
17. Casey S Greene
18. David E MacHugh

• Curated by eLife

  eLife Assessment

  This valuable study provides a proof of concept for the utility of transcriptomic methods to develop novel diagnostic tests for bovine tuberculosis. A comprehensive analysis using a suite of machine learning models provides convincing evidence for the use of mRNA biomarkers to distinguish between infected and disease-free animals. The analysis also provides major insights into both the levels of individual variation in expression between animals as well as systematic changes with respect to the time from infection.

Reviewed by eLife

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

1. Hanna Liao
2. Sanjay Kottapalli
3. Yuqi Huang
4. Matthew Chaw
5. Jase Gehring
6. Olivia Waltner
7. Melissa Phung-Rojas
8. Riza M Daza
9. Frederick A Matsen
10. Cole Trapnell
11. Jay Shendure
12. Sanjay Srivatsan

• Curated by eLife

  eLife Assessment

  This important technical study introduces SCOPE, an optics-free spatial reconstruction method based on bidirectional sender and receiver oligonucleotides on barcoded hydrogel beads. By sequencing proximity-encoded chimeric molecules, the authors computationally reconstruct 2D and 3D spatial information at an impressive scale. The technical demonstrations in synthetic bead systems are convincing and establish proof-of-principle that large spatial domains can be reconstructed without microscopy. The methodological advance is clear and the scale is impressive. This work will be of interest to those working on spatial mapping.

Reviewed by eLife

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific’s southernmost salmonid

1. Yi-Chien Lee
2. Zong-Yu Shen
3. Wei-Ren Lin
4. Tzi-Yuan Wang
5. Mark Liu
6. Yu-Chen Yeh
7. Shih-Fan Chan
8. Mei-Yeh Jade Lu
9. Hui-Yu Wang
10. Lin-Yan Liao
11. Wen-Hsiung Li
12. Jen-Pan Huang
13. Isheng Jason Tsai
14. Sheng-Feng Shen

• Curated by eLife

  eLife Assessment

  This valuable study combines a chromosome-level genome assembly with population resequencing and demographic modelling to reassess the status of the Formosan landlocked salmon, a critically endangered salmonid at the southern edge of the genus. The assembly and the evidence for extensive lineage-specific chromosomal fusions are genuinely well done, and the discovery of an overlooked, genetically distinct population in Hehuan Creek is sound and of clear management relevance. Evidence for the headline claims is incomplete: species rank is asserted but nowhere argued, and gene flow is excluded using a coalescent model that contains no migration parameter. Support for the population-viability conclusions is also not complete, as the demographic mechanisms invoked in the discussion are not borne out by the supplementary tables.

Reviewed by eLife

The genetic control of rapid genome content divergence in Arabidopsis thaliana

1. Christopher J Fiscus
2. Daniel Koenig

• Curated by eLife

  eLife Assessment

  This important study systematically investigates repeat expansion in the plant Arabidopsis thaliana using a new k-mer-based method, expanding on previous smaller studies, to comprehensively identify cis- and trans-acting loci associated with repeat dynamics. The approach is methodologically sound, and the exploration of different k-mer lengths and use of a more complete reference assembly strengthen confidence in the analysis while clarifying its limitations and the method is broadly applicable to large-scale short-read datasets for assessing copy-number variation and genomic repeat content. The findings are convincing in their scope and novelty for A. thaliana. It will be of interest to learn in future how the approach generalizes to species with substantially greater or lower repeat content.

Reviewed by eLife

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma

1. Olivia G Waltner
2. April A Apfelbaum
3. Emma D Wrenn
4. Shruti S Bhise
5. Sami B Kanaan
6. Rula Green Gladden
7. Mark A Mendoza
8. Roger Volden
9. Zev Kronenberg
10. Anand G Patel
11. Michael A Dyer
12. Jay F Sarthy
13. Elizabeth R Lawlor
14. Scott N Furlan

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of the gene regulatory networks that contribute to tumour heterogeneity and tumor plasticity in Ewing sarcoma, with key implications for other fusion-driven sarcomas. The authors employed compelling orthogonal approaches, including single-cell sequencing and xenografts, to reveal the existence and plasticity of specific gene regulatory networks (e.g., TGF-beta signaling) within Ewing sarcoma, as well as significant differences that exist between cell lines and patient tumors.

Reviewed by eLife

The cistrome response to hypoxia in human umbilical vein endothelial cells

1. Ayush Singh
2. Viktor Pastukh
3. Justin T Roberts
4. Zachary M Turpin
5. Zehta S Fazler
6. Grant T Daly
7. Jane M Benoit
8. Mark N Gillespie
9. Hank W Bass

• Curated by eLife

  eLife Assessment

  This is an important study that applies a new chromatin profiling technique to the study of cellular responses to low oxygen. The authors provide convincing evidence for distinct kinetic phases of the response and identify many new putative regulators of the response. This work will be of broad interest to those studying low oxygen responses and transcriptional regulation.

Reviewed by eLife

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

1. Fiona Teltscher
2. Petra Korlević
3. Edel Sheerin
4. Alex Makunin
5. Mara K N Lawniczak

Reviewed by GigaScience