Genomics

The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data

1. Hui-Su Kim
2. Asta Blazyte
3. Sungwon Jeon
4. Changhan Yoon
5. Yeonkyung Kim
6. Changjae Kim
7. Dan Bolser
8. Ji-Hye Ahn
9. Jeremy S. Edwards
10. Jong Bhak

Reviewed by GigaByte

Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis

1. Arnaud N’Guessan
2. Senthilkumar Kailasam
3. Fatima Mostefai
4. Raphael Poujol
5. Jean-Christophe Grenier
6. Paola Contini
7. Raffaele De Palma
8. Carsten Haber
9. Volker Stadler
10. Guillaume Bourque
11. Julie G. Hussin
12. B. Jesse Shapiro
13. Jörg H. Fritz
14. Ciriaco A. Piccirillo

Reviewed by ScreenIT

Single-nuclei characterization of pervasive transcriptional signatures across organs in response to COVID-19

1. The COVID Tissue Atlas Consortium
2. Alejandro A Granados
3. Simon Bucher
4. Hanbing Song
5. Aditi Agrawal
6. Ann T Chen
7. Tien Peng
8. Norma Neff
9. Angela Oliveira Pisco
10. Franklin Huang
11. Bruce Wang

• Curated by eLife

  eLife assessment

  This study provides a valuable data resource to study the systemic effects of severe COVID-19. It shows compelling evidence that the transcriptional response to COVID-19 is coordinated across the body, and it highlights cell interactions between macrophages and endothelial cells in COVID-19. This analysis and the associated resource will be valuable to understand the pathogenic mechanism of long-COVID.

Reviewed by eLife, ScreenIT

SARS-CoV-2 impacts the transcriptome and epigenome at the maternal-fetal interface in pregnancy

1. Lin Gao
2. Vrinda Mathur
3. Sabrina Ka Man Tam
4. Xuemeng Zhou
5. Ming Fung Cheung
6. Lu Yan Chan
7. Guadalupe Estrada-Gutiérrez
8. Bo Wah Leung
9. Sakita Moungmaithong
10. Chi Chiu Wang
11. Liona C. Poon
12. Danny Leung

Reviewed by ScreenIT

Genome similarities between human-derived and mink-derived SARS-CoV-2 make mink a potential reservoir of the virus

1. Mohammad Khalid
2. Yousef Al-ebini

Reviewed by ScreenIT

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial

1. Emma Peel
2. Luke Silver
3. Parice Brandies
4. Takashi Hayakawa
5. Katherine Belov
6. Carolyn J. Hogg

Reviewed by GigaByte

Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis

1. Sabriya A. Syed
2. Kristina Shqillo
3. Ankita Nand
4. Ye Zhan
5. Job Dekker
6. Anthony N. Imbalzano

• Curated by eLife

  eLife assessment

  How the genome is folded three dimensionally is thought to control gene regulatory pathways during critical processes such as cellular differentiation. Using multiple assays, the authors of this important study probe topologically associated domains (TADs) and report involvement of a protein arginine methyltransferase 5 in chromatin organization and transcriptional regulation. The data gathered are generally solid and broadly support the role of this protein in organization of the adipocytic lineage, but additional control experiments would make the inferences stronger.

Reviewed by eLife

The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS-CoV-2 coronavirus

1. José L. Oliver
2. Pedro Bernaola-Galván
3. Francisco Perfectti
4. Cristina Gómez Martín
5. Silvia Castiglione
6. Pasquale Raia
7. Miguel Verdú
8. Andrés Moya

Reviewed by ScreenIT

SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution

1. Urvashi B. Singh
2. Sushanta Deb
3. Rama Chaudhry
4. Kiran Bala
5. Lata Rani
6. Ritu Gupta
7. Lata Kumari
8. Jawed Ahmed
9. Sudesh Gaurav
10. Sowjanya Perumalla
11. Md. Nizam
12. Anwita Mishra
13. J. Stephenraj
14. Jyoti Shukla
15. Deepika Bhardwaj
16. Jamshed Nayer
17. Praveen Aggarwal
18. Madhulika Kabra
19. Vineet Ahuja
20. Subrata Sinha
21. Randeep Guleria

Reviewed by ScreenIT

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

1. Stefano G Giulieri
2. Romain Guérillot
3. Sebastian Duchene
4. Abderrahman Hachani
5. Diane Daniel
6. Torsten Seemann
7. Joshua S Davis
8. Steven YC Tong
9. Bernadette C Young
10. Daniel J Wilson
11. Timothy P Stinear
12. Benjamin P Howden

• Curated by eLife

  Evaluation Summary:

  This study offers a comprehensive examination of Staphylococcus aureus evolution during infection. This manuscript will be of broad interest to readers in the field of microbiology and infectious disease. It provides a useful analysis of a comprehensive set of genetic signatures of bacterial adaptation. A combination of multiple layers of genome annotation and point mutation variant detection compellingly supports the correlation of infection outcomes with adaptation signatures in S. aureus.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife