Genomics

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

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

1. Lara Urban
2. Allison K Miller
3. Daryl Eason
4. Deidre Vercoe
5. Megan Shaffer
6. Shaun P Wilkinson
7. Gert-Jan Jeunen
8. Neil J Gemmell
9. Andrew Digby

• Curated by eLife

  eLife assessment

  This work presents important findings regarding the use of soil environmental DNA for non-invasive monitoring of the endangered kākāpō parrot population in New Zealand. The approach based on sequence analysis is convincing but comparisons to established methods are lacking. The tools presented in this study are innovative and will be relevant to those working with environmental DNA and the conservation of biodiversity.

Reviewed by eLife

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies

1. Miguel A. Naranjo-Ortiz
2. Manu Molina
3. Verónica Mixão
4. Toni Gabaldón

Reviewed by GigaScience

A curated human cellular microRNAome based on 196 primary cell types

1. Arun H. Patil
2. Andrea Baran
3. Zachary P. Brehm
4. Matthew N. McCall
5. Marc K. Halushka

Reviewed by GigaScience

The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging

1. Monica Sanchez-Contreras
2. Mariya T Sweetwyne
3. Kristine A Tsantilas
4. Jeremy A Whitson
5. Matthew D Campbell
6. Brenden F Kohrn
7. Hyeon Jeong Kim
8. Michael J Hipp
9. Jeanne Fredrickson
10. Megan M Nguyen
11. James B Hurley
12. David J Marcinek
13. Peter S Rabinovitch
14. Scott R Kennedy

• Curated by eLife

  eLife assessment

  The analysis of 89,000 independent somatic mtDNA mutations provides compelling evidence that allows the authors to refute the idea that reactive oxygen species (ROS) are a main driver of mtDNA mutagenesis, although ROS effects may still be tissue-dependent. These are fundamental results with convincing evidence, and they should appeal to a broad audience. The discovery of transversion mutations (C>A/G>T and C>G/G>C), which previously were assumed to be almost nonexistent, will nevertheless require additional validation.

Reviewed by eLife

Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration

1. Caetano Souto-Maior
2. Yazmin L. Serrano Negron
3. Susan T. Harbison

Reviewed by Review Commons