Genomics

The first genome assembly of the amphibian nematode parasite ( Aplectana chamaeleonis )

1. Lei Han
2. Tianlu Liu
3. Fengping He
4. Zhijun Hou

Reviewed by GigaByte

Whole-genome sequencing of Chinese native goat offers biological insights into cashmere fiber formation

1. Hu Han
2. Man-Man Yang
3. Jiang Dan
4. Xing-Ju Zhang
5. Qiang Wei
6. Tao Chen
7. Qi-Ju Wang
8. Cheng-Ye Yang
9. Bater Wulan
10. Ting-Ting Zhang
11. Gang Gen
12. Mengkedala
13. Bin Li
14. Wei-Dong Deng
15. Ze-Pu Miao
16. Ran Wang
17. Qing-Feng Zhang
18. Lin Li
19. Sheng-Yu Chao
20. Ming Fang
21. Yong Li

Reviewed by GigaScience

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

1. Benjamin Guinet
2. David Lepetit
3. Sylvain Charlat
4. Peter N Buhl
5. David G Notton
6. Astrid Cruaud
7. Jean-Yves Rasplus
8. Julia Stigenberg
9. Damien M de Vienne
10. Bastien Boussau
11. Julien Varaldi

• Curated by eLife

  eLife assessment

  This important manuscript employs a rigorous and multi-pronged comparative genomics approach to unravel how lifestyle modulates the acquisition and domestication of viral genetic elements in the genomes of hymenopteran insects. Using an extensive dataset of over 120 hymenopteran genomes, the authors provide convincing evidence that endoparasitism (where parasite development occurs within hosts) facilitates the uptake and domestication of double-stranded DNA viral elements.

Reviewed by eLife

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