Genomics

Chromosome-level genome assemblies of five Sinocyclocheilus species

1. Chao Bian
2. Ruihan Li
3. Yuqian Ouyang
4. Junxing Yang
5. Xidong Mu
6. Qiong Shi

• Curated by GigaByte

  **Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

1. Yered Pita-Juarez
2. Dimitra Karagkouni
3. Nikolaos Kalavros
4. Johannes C. Melms
5. Sebastian Niezen
6. Toni M. Delorey
7. Adam L. Essene
8. Olga R. Brook
9. Deepti Pant
10. Disha Skelton-Badlani
11. Pourya Naderi
12. Pinzhu Huang
13. Liuliu Pan
14. Tyler Hether
15. Tallulah S. Andrews
16. Carly G. K. Ziegler
17. Jason Reeves
18. Andriy Myloserdnyy
19. Rachel Chen
20. Andy Nam
21. Stefan Phelan
22. Yan Liang
23. Mark Gregory
24. Shanshan He
25. Michael Patrick
26. Tushar Rane
27. Aster Wardhani
28. Amit Dipak Amin
29. Jana Biermann
30. Hanina Hibshoosh
31. Molly Veregge
32. Zachary Kramer
33. Christopher Jacobs
34. Yusuf Yalcin
35. Devan Phillips
36. Michal Slyper
37. Ayshwarya Subramanian
38. Orr Ashenberg
39. Zohar Bloom-Ackermann
40. Victoria M. Tran
41. James Gomez
42. Alexander Sturm
43. Shuting Zhang
44. Stephen J. Fleming
45. Sarah Warren
46. Joseph Beechem
47. Deborah Hung
48. Mehrtash Babadi
49. Robert F. Padera
50. Sonya A. MacParland
51. Gary D. Bader
52. Nasser Imad
53. Isaac H. Solomon
54. Eric Miller
55. Stefan Riedel
56. Caroline B. M. Porter
57. Alexandra-Chloé Villani
58. Linus T.-Y. Tsai
59. Winston Hide
60. Gyongyi Szabo
61. Jonathan Hecht
62. Orit Rozenblatt-Rosen
63. Alex K. Shalek
64. Benjamin Izar
65. Aviv Regev
66. Yury V. Popov
67. Z. Gordon Jiang
68. Ioannis S. Vlachos

Reviewed by Rapid Reviews Infectious Diseases

Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

1. Hisato Kobayashi
2. Tatsushi Igaki
3. Soichiro Kumamoto
4. Keisuke Tanaka
5. Tomoya Takashima
6. So I Nagaoka
7. Shunsuke Suzuki
8. Masaaki Hayashi
9. Marilyn B Renfree
10. Manabu Kawahara
11. Shun Saito
12. Toshihiro Kobayashi
13. Hiroshi Nagashima
14. Hitomi Matsunari
15. Kazuaki Nakano
16. Ayuko Uchikura
17. Hiroshi Kiyonari
18. Mari Kaneko
19. Hiroo Imai
20. Kazuhiko Nakabayashi
21. Matthew Lorincz
22. Kazuki Kurimoto

• Curated by eLife

  eLife Assessment

  The authors analyses describe a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting and demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. This imprinting of the ZDBF2 locus correlates with transcription of GPR1-AS orthologs. The accompanying genomic analysis is very well executed allowing for the conclusions reached in the manuscript. The revisions made at the request of the reviewers in this important manuscript strengthen the evidence from the genomic analyses, and as a result, the evidence is now convincing and will be informative to the genomics and developmental biology communities.

Reviewed by eLife

OTX2 controls chromatin accessibility to direct somatic versus germline differentiation

1. Elisa Barbieri
2. Ian Chambers

Reviewed by Review Commons

Transcription can be sufficient, but is not necessary, to advance replication timing

1. Athanasios E. Vouzas
2. Takayo Sasaki
3. Juan Carlos Rivera-Mulia
4. Jesse L. Turner
5. Amber N. Brown
6. Karen E. Alexander
7. Laura Brueckner
8. Bas van Steensel
9. David M. Gilbert

Reviewed by Review Commons

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

1. Jingzhong Xie
2. Qiaoling Luo
3. Limin Wang
4. Dan Qiu
5. Caihong Zhao
6. Jinghuang Hu
7. Jing Zhang
8. Xinyu Zhao
9. Zhaogen Chen
10. Yibo Wang
11. Yang Yu
12. Mengzhen Luo
13. Haoyuan Song
14. Yuexuan Hou
15. Zhimeng Zhang
16. Mou Yin
17. Haojie Wang
18. Xuanzhao Li
19. Xiaomeng Fu
20. Bei Xiao
21. Yahui Li
22. Jiajie Wu
23. Wenxuan Liu
24. Yanpeng Wang
25. Mo Zhu
26. Yanming Zhang
27. Alisdair R. Fernie
28. Wei Wang
29. Hongjie Li
30. Fei He

Reviewed by PREreview

Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome

1. Wenliang Wang
2. Manoj Hariharan
3. Wubin Ding
4. Anna Bartlett
5. Cesar Barragan
6. Rosa Castanon
7. Vince Rothenberg
8. Haili Song
9. Joseph Nery
10. Andrew Aldridge
11. Jordan Altshul
12. Mia Kenworthy
13. Hanqing Liu
14. Wei Tian
15. Jingtian Zhou
16. Qiurui Zeng
17. Huaming Chen
18. Bei Wei
19. Irem B. Gündüz
20. Todd Norell
21. Timothy J Broderick
22. Micah T. McClain
23. Lisa L. Satterwhite
24. Thomas W. Burke
25. Elizabeth A. Petzold
26. Xiling Shen
27. Christopher W. Woods
28. Vance G. Fowler
29. Felicia Ruffin
30. Parinya Panuwet
31. Dana B. Barr
32. Jennifer L. Beare
33. Anthony K. Smith
34. Rachel R. Spurbeck
35. Sindhu Vangeti
36. Irene Ramos
37. German Nudelman
38. Stuart C. Sealfon
39. Flora Castellino
40. Anna Maria Walley
41. Thomas Evans
42. Fabian Müller
43. William J. Greenleaf
44. Joseph R. Ecker

Reviewed by Rapid Reviews Infectious Diseases

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

1. Hewei Liang
2. Yuanqiang Zou
3. Mengmeng Wang
4. Tongyuan Hu
5. Haoyu Wang
6. Wenxin He
7. Yanmei Ju
8. Ruijin Guo
9. Junyi Chen
10. Fei Guo
11. Tao Zeng
12. Yuliang Dong
13. Yuning Zhang
14. Bo Wang
15. Chuanyu Liu
16. Xin Jin
17. Wenwei Zhang
18. Xun Xu
19. Liang Xiao

• Curated by GigaByte

  Editors Assessment:

  With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

1. Joyner Cruz
2. Willam Y Sun
3. Alexandra Verbeke
4. Iswar K Hariharan

• Curated by eLife

  eLife Assessment

  This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to assess heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila. A cell cycle based clustering approach allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their convincing analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

Reviewed by eLife

Convergent evolution of epigenome recruited DNA repair across the Tree of Life

1. J Grey Monroe
2. Chaehee Lee
3. Daniela Quiroz
4. Mariele Lensink
5. Satoyo Oya
6. Matthew Davis
7. Evan Long
8. Kevin A Bird
9. Alice Pierce
10. Kehan Zhao
11. Daniel Runcie

• Curated by eLife

  eLife Assessment

  This paper describes the study of the evolution of the N-terminal domain of the MSH6 mismatch repair protein in regard to the presence or absence of histone reader domains. While the presence of the histone reader domains was previously known, the phylogenetic analysis of these domains performed here establishing their insertion through convergent evolution is important, definitively done, and establishes an interesting feature of the MSH6 family of proteins. The work is convincing but the presentation of the structural features of MSH6 could be improved.

Reviewed by eLife