Genomics

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

1. William Matlock
2. Samuel Lipworth
3. Kevin K Chau
4. Manal AbuOun
5. Leanne Barker
6. James Kavanagh
7. Monique Andersson
8. Sarah Oakley
9. Marcus Morgan
10. Derrick W Crook
11. Daniel S Read
12. Muna Anjum
13. Liam P Shaw
14. Nicole Stoesser
15. REHAB Consortium

• Curated by eLife

  eLife assessment

  This important study presents valuable findings on the dissemination of plasmids. In an analysis of five major Enterobacterales genera, the authors convincingly demonstrate that similar plasmids are shared between genera, species, and clones, both within and between ecological niches. Given the size of the dataset and the very detailed level of analysis this study importantly contributes to insights into to the flow of plasmids, including those carrying antimicrobial resistance genes, across niches.

Reviewed by eLife

Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

1. Jeff Jiajing Zhou
2. Jin Sun Cho
3. Han Han
4. Ira L Blitz
5. Wenqi Wang
6. Ken WY Cho

• Curated by eLife

  eLife assessment

  In this manuscript, the authors investigate the role of histone deacetylases in the spatial epigenetic control of zygotic gene expression in early gastrulation. They discover HDAC1 binding is maternally-controlled and that inhibition of histone acetylation blocks gastrulation and disrupts cell lineage integrity, tied to both positive and negative regulatory effects on gene transcription in space and time. The study contributes to a growing body of evidence that highlights a central role of histone acetylation-deacetylation dynamics in epigenetic regulation of gene expression and cell fating in early tissue patterning of the embryo.

Reviewed by eLife

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

1. Jeremiah Miller
2. Aleksey V Zimin
3. Andrew Gordus

Reviewed by GigaScience

A molecular phenotypic map of malignant pleural mesothelioma

1. Alex Di Genova
2. Lise Mangiante
3. Alexandra Sexton-Oates
4. Catherine Voegele
5. Lynnette Fernandez-Cuesta
6. Nicolas Alcala
7. Matthieu Foll

Reviewed by GigaScience

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

1. Harsh Shukla
2. Kushal Suryamohan
3. Anubhab Khan
4. Krishna Mohan
5. Rajadurai C Perumal
6. Oommen K Mathew
7. Ramesh Menon
8. Mandumpala Davis Dixon
9. Megha Muraleedharan
10. Boney Kuriakose
11. Saju Michael
12. Sajesh P Krishnankutty
13. Arun Zachariah
14. Somasekar Seshagiri
15. Uma Ramakrishnan

Reviewed by GigaScience

A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

1. Hongbo Wang
2. Hin Ting Wan
3. Bin Wu
4. Jianbo Jian
5. Alice HM Ng
6. Claire Yik-Lok Chung
7. Eugene Yui-Ching Chow
8. Jizhou Zhang
9. Anderson OL Wong
10. Keng Po Lai
11. Ting Fung Chan
12. Eric Lu Zhang
13. Chris Kong-Chu Wong

Reviewed by GigaScience

Effects of smoking on genome-wide DNA methylation profiles: A study of discordant and concordant monozygotic twin pairs

1. Jenny van Dongen
2. Gonneke Willemsen
3. BIOS Consortium
4. Eco JC de Geus
5. Dorret I Boomsma
6. Michael C Neale

• Curated by eLife

  eLife assessment

  This study presents valuable findings from a study of identical twin pairs discordant and concordant for smoking to assess whether smoking has a direct effect on DNA methylation. The results are a valuable contribution as the study confirms the reported association between smoking and epigenetic profile is indeed due to the direct effects of constituents of tobacco smoke. The study design and methods applied by the authors are solid and provide a starting point for larger studies with rigorous laboratory approaches, as well as for assessing clinical impact. The work will be of broad interest to addiction researchers, genetic epidemiologists, and environmental scientists.

Reviewed by eLife

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

1. Hollis A Dahn
2. Jacquelyn Mountcastle
3. Jennifer Balacco
4. Sylke Winkler
5. Iliana Bista
6. Anthony D Schmitt
7. Olga Vinnere Pettersson
8. Giulio Formenti
9. Karen Oliver
10. Michelle Smith
11. Wenhua Tan
12. Anne Kraus
13. Stephen Mac
14. Lisa M Komoroske
15. Tanya Lama
16. Andrew J Crawford
17. Robert W Murphy
18. Samara Brown
19. Alan F Scott
20. Phillip A Morin
21. Erich D Jarvis
22. Olivier Fedrigo

Reviewed by GigaScience

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

1. B Ramesh
2. CM Small
3. H Healey
4. B Johnson
5. E Barker
6. M Currey
7. S Bassham
8. M Myers
9. WA Cresko
10. AG Jones

Reviewed by GigaByte

Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions

1. Carol A Edwards
2. William MD Watkinson
3. Stephanie B Telerman
4. Lisa C Hulsmann
5. Russell S Hamilton
6. Anne C Ferguson-Smith

• Curated by eLife

  eLife assessment

  This manuscript presents a useful meta-analysis of genes with parent-specific expression from mouse published RNA-seq datasets, focusing on genes with weak allelic bias. A combination of systematic bioinformatic analysis and experimental validation convincingly shows that the number of parentally biased genes has been overestimated and the few novel ones lie at the periphery of known imprinted loci. The work will be of interest to genomicists with an interest in imprinting and its mechanisms.

Reviewed by eLife