Genomics

DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A

1. Ioannis Kafetzopoulos
2. Francesca Taglini
3. Hazel Davidson-Smith
4. Duncan Sproul

Reviewed by Review Commons

Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia

1. Trinity Conn
2. Jill Ashey
3. Ross Cunning
4. Hollie M. Putnam

• Curated by GigaByte

  Editors Assessment:

  Acropora pulchra is a species small polyped stony corals in the family Acroporidae from the the Indo-Pacific. This Data Release is the first study in stony corals to present the DNA methylome in tandem with a high-quality genome assembled utilizing PacBio long-read HiFi sequencing. Sequencing an A. pulchra specimen from Mo’orea, French Polynesia. From this single molecule sequencing data DNA methylation data was also called and quantified, and additional short-read Illumina RNASeq data was used for gene annotation. This producing an assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp, and 40,518 protein-coding genes called. Peer review requested some improved benchmarking, and it is impressive to see from the results that the genome assembly represents the most complete and contiguous stony coral genome assembly to date. As an important indicator species and this data will hopefully serve as a resource to the coral and wider scientific community. Further quantification of the genome-wide methylation is needed aid the study epigenetics of non-model organisms, and specifically future analyses on methylation in coral.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations

1. Lucas Inchausti
2. Lucía Bilbao
3. Vanina A Campo
4. Joaquín Garat
5. José Sotelo-Silveira
6. Gabriel Rinaldi
7. Virginia M Howick
8. María Ana Duhagon
9. Javier G De Gaudenzi
10. Pablo Smircich

• Curated by eLife

  eLife Assessment

  This important study utilizes single-cell RNA sequencing to reveal the heterogeneity of trans-sialidase-like superfamily gene expression in Trypanosoma cruzi populations. The approach is highly convincing, as it successfully assigns cells to specific developmental forms and highlights the variability in surface protein expression among trypomastigotes. However, while the findings are solid and contribute to the understanding of immune evasion mechanisms, the study would benefit from a more detailed exploration of the regulatory factors governing trans-sialidase expression. Strengthening this aspect would further enhance its impact on researchers studying T. cruzi pathogenesis and host-parasite interactions.

Reviewed by eLife

Genome modeling and design across all domains of life with Evo 2

1. Garyk Brixi
2. Matthew G. Durrant
3. Jerome Ku
4. Michael Poli
5. Greg Brockman
6. Daniel Chang
7. Gabriel A. Gonzalez
8. Samuel H. King
9. David B. Li
10. Aditi T. Merchant
11. Mohsen Naghipourfar
12. Eric Nguyen
13. Chiara Ricci-Tam
14. David W. Romero
15. Gwanggyu Sun
16. Ali Taghibakshi
17. Anton Vorontsov
18. Brandon Yang
19. Myra Deng
20. Liv Gorton
21. Nam Nguyen
22. Nicholas K. Wang
23. Etowah Adams
24. Stephen A. Baccus
25. Steven Dillmann
26. Stefano Ermon
27. Daniel Guo
28. Rajesh Ilango
29. Ken Janik
30. Amy X. Lu
31. Reshma Mehta
32. Mohammad R.K. Mofrad
33. Madelena Y. Ng
34. Jaspreet Pannu
35. Christopher Ré
36. Jonathan C. Schmok
37. John St. John
38. Jeremy Sullivan
39. Kevin Zhu
40. Greg Zynda
41. Daniel Balsam
42. Patrick Collison
43. Anthony B. Costa
44. Tina Hernandez-Boussard
45. Eric Ho
46. Ming-Yu Liu
47. Thomas McGrath
48. Kimberly Powell
49. Dave P. Burke
50. Hani Goodarzi
51. Patrick D. Hsu
52. Brian L. Hie

Reviewed by Life Science Editors Foundation, Arcadia Science

Pyruvate and Related Energetic Metabolites Modulate Resilience Against High Genetic Risk for Glaucoma

1. Keva Li
2. Nicholas Tolman
3. Ayellet V Segrè
4. Kelsey V Stuart
5. Oana A Zeleznik
6. Neeru A Vallabh
7. Kuang Hu
8. Nazlee Zebardast
9. Akiko Hanyuda
10. Yoshihiko Raita
11. Christa Montgomery
12. Chi Zhang
13. Pirro G Hysi
14. Ron Do
15. Anthony P Khawaja
16. Janey L Wiggs
17. Jae H Kang
18. Simon WM John
19. Louis R Pasquale
20. UK Biobank Eye and Vision Consortium

• Curated by eLife

  eLife Assessment

  This study presents a valuable finding on the importance of the plasma metabolome in glaucoma risk prediction. The evidence supporting the claims of the authors is solid and the work offers insights for the design of protective therapeutic strategies for glaucoma. The authors have addressed the concerns of the reviewers and reported on the limitations of the study.

Reviewed by eLife

Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial development

1. Theresa Schmid
2. Gabriele Rodrian
3. Alexander Kohler
4. Michael Wegner
5. Lina Gölz
6. Matthias Weider

Reviewed by Review Commons

Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

1. Omid Gholamalamdari
2. Tom van Schaik
3. Yuchuan Wang
4. Pradeep Kumar
5. Liguo Zhang
6. Yang Zhang
7. Gabriela A Hernandez Gonzalez
8. Athanasios E Vouzas
9. Peiyao A Zhao
10. David M Gilbert
11. Jian Ma
12. Bas van Steensel
13. Andrew S Belmont

• Curated by eLife

  eLife Assessment

  In this valuable study, the authors integrate several datasets to describe how the genome interacts with nuclear bodies across distinct cell types and in Lamin A and LBR knockout cells. They provide convincing evidence to support their claims and particularly find that specific genomic regions segregate relative to the equatorial plane of the cell when considering their interaction with various nuclear bodies.

Reviewed by eLife

Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora

1. Julia D Sigwart
2. Yunlong Li
3. Zeyuan Chen
4. Katarzyna Vončina
5. Jin Sun

• Curated by eLife

  eLife Assessment

  This important study advances our understanding of genome annotations for chiton genomes. It provides a solid estimation of syntentic relationships for the chromosomes of the four new genomes plus an analysis linking these to other available chiton genomes, and an update for how these relate to molluscan genomes.

Reviewed by eLife

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species

1. Ma. Carmel F. Javier
2. Albert C. Noblezada
3. Persie Mark Q. Sienes
4. Robert S. Guino-o
5. Nadia Palomar-Abesamis
6. Maria Celia D. Malay
7. Carmelo S. del Castillo
8. Victor Marco Emmanuel N. Ferriols

• Curated by GigaByte

  Editors Assessment:

  The Visayan spotted deer (Rusa alfredi), is a small, endangered, primarily nocturnal species of deer found in the rainforests of the Visayan Islands in the Philippines. The present study reports the first draft genome assembly for the species, addressing a critical gap in genomic data for this IUCN-redlisted cervid. Using Illumina sequencing, the resulting genome assembly spans 2.52 Gb in size with a BUSCO completeness score of 95.5% and encompasses 24,531 annotated genes. Phylogenetic analysis suggests a close evolutionary relationship between R. alfredi and Cervus species suggesting that the genus Rusa is sister to Cervus. Peer-review teased out more benchmarking results and the annotation files, demonstrating this genomic resource is useful and usable for advancing population genetics and evolutionary studies, thereby informing conservation strategies and enhancing breeding programs for the critically threatened species. Providing whole genome sequences for other native species of Rusa could further provide genomic resources for detecting hybrids, which will also help the management and monitoring of these species, especially for the reintroduction of captive populations in the wild.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

1. Eleanore J. Ritter
2. Noé Cochetel
3. Andrea Minio
4. Peter Cousins
5. Dario Cantu
6. Chad Niederhuth

• Curated by GigaByte

  Editors Assessment:

  Teinturier grapes produce berries with pigmented skin and flesh, and are used in red wine blends, as they provide a deeper colour. This paper presents the genomes of two popular teinturier varieties (Dakapo and Rubired); sequenced, assembled, and annotated to provide additional resources for their use in breeding. Combining Nanopore and Illumina sequencing for Dakapo, scaffolding to the existing grapevine assembly to generate a final assembly of 508.5 Mbp and 36,940 gene annotations. For Rubired PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long and 56,681 genes annotated. Peer review has helped validate their high quality, these genomes hopefully enabling more insight into the genetics of grapevine berry colour and their other traits like frost and mildew-resistance.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte