Genomics

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

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

1. John T Lovell
2. Avinash Sreedasyam
3. M Eric Schranz
4. Melissa Wilson
5. Joseph W Carlson
6. Alex Harkess
7. David Emms
8. David M Goodstein
9. Jeremy Schmutz

• Curated by eLife

  Evaluation Summary:

  This manuscript describing GENESPACE was found to be of high interest for the genomics community across many different fields. GENESPACE is a new and straightforward computational tool to include synteny information in the calculation of genome-wide sets of orthologs. This is very timely as more and more chromosome-scale assembled genomes are becoming available.

  (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. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Activated interstitial macrophages are a predominant target of viral takeover and focus of inflammation in COVID-19 initiation in human lung

1. Timothy Ting-Hsuan Wu
2. Kyle J. Travaglini
3. Arjun Rustagi
4. Duo Xu
5. Yue Zhang
6. Leonid Andronov
7. SoRi Jang
8. Astrid Gillich
9. Roozbeh Dehghannasiri
10. Giovanny Martínez-Colón
11. Aimee Beck
12. Daniel Dan Liu
13. Aaron J. Wilk
14. Maurizio Morri
15. Winston L. Trope
16. Rob Bierman
17. Irving L. Weissman
18. Joseph B. Shrager
19. Stephen R. Quake
20. Christin S. Kuo
21. Julia Salzman
22. W. E. Moerner
23. Peter S. Kim
24. Catherine A. Blish
25. Mark A. Krasnow

Reviewed by ScreenIT

Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection

1. Martin Jankowiak
2. Fritz H. Obermeyer
3. Jacob E. Lemieux

Reviewed by ScreenIT

Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for human bone mineral density GWAS associations

1. Basel Maher Al-Barghouthi
2. Will T Rosenow
3. Kang-Ping Du
4. Jinho Heo
5. Robert Maynard
6. Larry Mesner
7. Gina Calabrese
8. Aaron Nakasone
9. Bhavya Senwar
10. Louis Gerstenfeld
11. James Larner
12. Virginia Ferguson
13. Cheryl Ackert-Bicknell
14. Elise Morgan
15. David Brautigan
16. Charles R Farber

• Curated by eLife

  Evaluation Summary:

  This manuscript is of broad interest to geneticists and bone biologists because it describes a method to filter candidate genes, identified from GWAS, and pinpoint the gene that affects bone biology. This method identified a gene with a previously unknown role in bone biology and the authors showed that its loss reduces bone mineral density, supporting the key claims in the paper.

  (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 #2 agreed to share their name with the authors.)

Reviewed by eLife