Genomics

Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics

1. Thibault Leroy
2. Elise Albert
3. Tatiana Thouroude
4. Sylvie Baudino
5. Jean-Claude Caissard
6. Annie Chastellier
7. Jérôme Chameau
8. Julien Jeauffre
9. Thérèse Loubert
10. Saretta Nindya Paramita
11. Alix Pernet
12. Vanessa Soufflet-Freslon
13. Cristiana Oghina-Pavie
14. Fabrice Foucher
15. Laurence Hibrand-Saint Oyant
16. Jérémy Clotault

Reviewed by Peer Community in Evolutionary Biology

Methylation Clocks Do Not Predict Age or Alzheimer’s Disease Risk Across Genetically Admixed Individuals

1. Sebastián Cruz-González
2. Esther Gu
3. Lissette Gomez
4. Makaela Mews
5. Jeffery M Vance
6. Michael L Cuccaro
7. Mario R Cornejo-Olivas
8. Briseida E Feliciano-Astacio
9. Goldie S Byrd
10. Jonathan L Haines
11. Margaret A Pericak-Vance
12. Anthony J Griswold
13. William S Bush
14. John A Capra

• Curated by eLife

  eLife Assessment

  This valuable study assesses epigenetic clocks across ancestries, including in the context of accelerated aging in Alzheimer's Disease patients. It provides convincing evidence for population differences in age estimation accuracy across a variety of epigenetic clocks, but the degree to which these differences reflect continuous variation in ancestry, and/or are confounded by environmental or power differences is not entirely clear; consequently, the evidence that reduced portability is rooted in genetics is incomplete. Given the accelerating use of epigenetic clocks across fields, this study is nevertheless likely to be of interest to researchers working on human genetic and epigenetic variation or who apply epigenetic clocks to diverse human populations.

Reviewed by eLife

Adenine DNA methylation associated to transcription is widespread across eukaryotes

1. Pedro Romero Charria
2. Cristina Navarrete
3. Vladimir Ovchinnikov
4. Luke A Sarre
5. Victoria Shabardina
6. Elena Casacuberta
7. David Lara-Astiaso
8. Arnau Sebé-Pedrós
9. Alex de Mendoza

Reviewed by preLights

Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes

1. Shuai Zhang
2. Ruixue Wang
3. Kun Luo
4. Shipeng Gu
5. Xinyu Liu
6. Junhan Wang
7. Ludan Zhang
8. Lin Sun

• Curated by eLife

  eLife Assessment

  This valuable study suggests that the dosage compensation complex and m6A act in a feedback loop in Drosophila melanogaster. The study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, which suggests that m6A modification status may influence H3K16Ac deposition through regulation of the acetyltransferase MOF. However, it is not clear whether this regulation is directly or indirectly related to m6A regulation. The evidence is considered incomplete due to technical concerns, as quantitative assessments were made using non-quantitative methods.

Reviewed by eLife

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

1. Emma Gairin
2. Saori Miura
3. Hiroki Takamiyagi
4. Marcela Herrera
5. Vincent Laudet

• Curated by GigaByte

  Editors Assessment:

  Among hot topics in coral reef research, the difference between anemonefish and other damselfish is currently a popular area of research. In this study the authors provide a new high-quality non-anemonefish genome, which will be of high relevance to further the depth of such analyses. In this case of the sapphire damselfish Chrysiptera cyanea, a widely distributed damselfish in the Indo-Pacific area, often studied to elucidate the roles of various environmental controls on their reproduction, and investigate related hormonal processes To further the potential of biomolecular analyses based on this species, this study generated the first genome of a Chrysiptera fish from a male individual collected in Okinawa, Japan. Using PacBio and HiFI long-read sequencing with 94.5x coverage, a chromosome-scale genome was assembled and 28,173 genes identified and annotated. Peer review gathered more parameters and details on the quality, and the final assembly comprised of 896 Mb pairs across 91 contigs, and a BUSCO completeness of 97.6%. This reference genome should therefore be of high value for future genetic-based approaches, from population structure to gene expression analyses.
  

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

1. Torsten Günther
2. Jacob Chisausky
3. Ángeles M Galindo-Pellicena
4. Eneko Iriarte
5. Oscar Cortes Gardyn
6. Paulina G Eusebi
7. Rebeca García-González
8. Irene Ureña
9. Marta Moreno-García
10. Alfonso Alday
11. Manuel Rojo
12. Amalia Pérez
13. Cristina Tejedor Rodríguez
14. Iñigo García Martínez de Lagrán
15. Juan Luis Arsuaga
16. José-Miguel Carretero
17. Anders Götherström
18. Colin Smith
19. Cristina Valdiosera

• Curated by eLife

  eLife Assessment

  Using genomic data from ancient and modern samples, this important study investigates the genomic history of cattle in Iberia, focusing on the admixture between domestic cattle and their wild ancestors, aurochs. The authors present convincing evidence for interbreeding between domestic cattle and wild aurochs since the Neolithic period, although the evidence of sex-biased introgression is weak. The authors also show that the aurochs ancestry in cattle stabilized at ~20% since ~4000 years ago and continues into modern breeds; however, the aurochs ancestry is not heightened in a modern breed of Spanish fighting bulls that are bred for aggressiveness. The work will be of interest to evolutionary biologists and quantitative geneticists who seek to understand the genomic history and genetic basis of trait variation of domesticated animals.

Reviewed by eLife

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

1. Kira Breunig
2. Xuifen Lei
3. Mauro Montalbano
4. Gabriela DA Guardia
5. Shiva Ostadrahimi
6. Victoria Alers
7. Adam Kosti
8. Jennifer Chiou
9. Nicole Klein
10. Corina Vinarov
11. Lily Wang
12. Mujia Li
13. Weidan Song
14. W Lee Kraus
15. David S Libich
16. Stefano Tiziani
17. Susan T Weintraub
18. Pedro AF Galante
19. Luiz O Penalva

• Curated by eLife

  eLife Assessment

  This study reports valuable insights into the interactome of the RNA-binding protein SERBP1 and possible links through PARylation to diverse processes, including splicing, cell division, and ribosome biogenesis. The diversity of processes SERBP1 may regulate means this work would be of very broad interest to the cell biology community. The proteomics data are solid, but the functional connection to downstream processes and the link to Alzheimer's disease, while compelling, still require further examination. These latter data currently rely on a very limited set of experiments and patient samples with questionable quality of preservation and methodology.

Reviewed by eLife

Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies

1. Jorge Blanco Mendana
2. Margaret Donovan
3. Lindsey Gengelbach O'Brien
4. Benjamin Auch
5. John Garbe
6. Daryl M Gohl

• Curated by eLife

  eLife Assessment

  This useful study presents a genetically encoded barcoding system that could advance transcriptomic studies and that has the potential for further applications, such as in high-throughput population-scale behavioral measurements. The evidence supporting the claims of the authors is solid and highlights both the usefulness and the limitations of the approach.

Reviewed by eLife

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

1. Mehul Vora
2. Jonathan Dietz
3. Zachary Wing
4. Karen George
5. Jun Kelly Liu
6. Christopher Rongo
7. Cathy Savage-Dunn

• Curated by eLife

  eLife Assessment

  Modulation of BMP signalling affects body size in the nematode Caenorhabditis elegans, and this paper examines the effects on C. elegans body size brought about by the modulation of BMP signalling. Thw study provides valuable analyses of ChIP-seq and RNA-Seq data to understand the function of SMA-3 (Smad) and SMA-9 (Schnurri) in this model. The authors provide compelling evidence that the BMP-dependent body size effect could be due to defects in cuticle collagen secretion, a finding of interest to those studying organismal growth and epidermal function.

Reviewed by eLife

Non-linear transcriptional responses to gradual modulation of transcription factor dosage

1. Júlia Domingo
2. Mariia Minaeva
3. John A Morris
4. Sam Ghatan
5. Marcello Ziosi
6. Neville E Sanjana
7. Tuuli Lappalainen

• Curated by eLife

  eLife Assessment

  This important work develops a new protocol to experimentally perturb target genes across a quantitative range of expression levels in cell lines. The evidence supporting their new perturbation approach is compelling, and the computational analyses to better understand dosage response relationships between genes are convincing. The study will be of broad interest to scientists in the fields of functional genomics and biotechnology. However, the evidence supporting the conclusions can be further improved.

Reviewed by eLife