Genomics

Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

1. Santiago Justo Arevalo
2. Daniela Zapata Sifuentes
3. César J. Huallpa
4. Gianfranco Landa Bianchi
5. Adriana Castillo Chávez
6. Romina Garavito-Salini Casas
7. Carmen Sofia Uribe Calampa
8. Guillermo Uceda-Campos
9. Roberto Pineda Chavarría

Reviewed by ScreenIT

Relating multivariate shapes to genescapes using phenotype-biological process associations for craniofacial shape

1. Jose D Aponte
2. David C Katz
3. Daniela M Roth
4. Marta Vidal-García
5. Wei Liu
6. Fernando Andrade
7. Charles C Roseman
8. Steven A Murray
9. James Cheverud
10. Daniel Graf
11. Ralph S Marcucio
12. Benedikt Hallgrímsson

• Curated by eLife

  Evaluation Summary:

  This paper offers a new take on multivariate genotype-phenotype mapping that identifies the joint phenotypic effect of genes involved in known biological processes that impact craniofacial variation. More specifically, the work expands on the traditional idea of candidate gene investigations into candidate biological process investigations, grouping multiple genes into a single analysis. In doing so, the authors show the joint effects of three strong candidate processes, chondrocyte differentiation, determination of left/right symmetry, and palate development on multidimensional craniofacial shape in the heterogenous Diversity Outbred mouse population.

  (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 names with the authors.)

Reviewed by eLife

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

1. Nathan Smits
2. Jay Rasmussen
3. Gabriela O. Bodea
4. Alberto A. Amarilla
5. Patricia Gerdes
6. Francisco J. Sanchez-Luque
7. Prabha Ajjikuttira
8. Naphak Modhiran
9. Benjamin Liang
10. Jamila Faivre
11. Ira W. Deveson
12. Alexander A. Khromykh
13. Daniel Watterson
14. Adam D. Ewing
15. Geoffrey J. Faulkner

Reviewed by ScreenIT

Computational genomic analysis of the lung tissue microenvironment in COVID-19 patients

1. Krithika Bhuvaneshwar
2. Subha Madhavan
3. Yuriy Gusev

Reviewed by ScreenIT

Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential

1. Slawomir Kubik
2. Nils Arrigo
3. Jaume Bonet
4. Zhenyu Xu

Reviewed by ScreenIT

Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh

1. Abdullah Al Nahid
2. Ajit Ghosh

Reviewed by ScreenIT

Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19

1. Poonam Mehta
2. Saumya Sarkar
3. Ujjala Ghoshal
4. Ankita Pandey
5. Ratender Singh
6. Dharamveer Singh
7. Rahul Vishvkarma
8. Uday Chand Ghoshal
9. Ranjeet Maurya
10. Rajesh Pandey
11. Ravishankar Ramachandran
12. Punyasloke Bhadury
13. Tapas K Kundu
14. Singh Rajender

Reviewed by ScreenIT

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

1. Ursula Oggenfuss
2. Thomas Badet
3. Thomas Wicker
4. Fanny E Hartmann
5. Nikhil Kumar Singh
6. Leen Abraham
7. Petteri Karisto
8. Tiziana Vonlanthen
9. Christopher Mundt
10. Bruce A McDonald
11. Daniel Croll

• Curated by eLife

  Evaluation Summary:

  This study is of potential interest to a broad audience on evolutionary and population genomics, particularly scientists studying genome dynamics, including transposable elements (TE) and their evolution. It takes advantage of genomics datasets from a large population of wheat pathogens collected across the globe at different times (decades) to detect ongoing processes of genome expansion and potential selection mediated by TE insertions. The work provides empirical evidence that drastic demographic processes shape TE dynamics in nature and that these contribute to intraspecific variation in genome sizes, recapitulating the well-stablished association between TE content and genome size observed across the diversity of life forms.

  (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

1. Dilan SR Patiranage
2. Elodie Rey
3. Nazgol Emrani
4. Gordon Wellman
5. Karl Schmid
6. Sandra M Schmöckel
7. Mark Tester
8. Christian Jung

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive study of genomic and phenotypic diversity in the orphan crop quinoa. Based on whole genome resequencing of 310 accessions and field phenotyping of the same set of accessions for two years, the study identified the genetic basis of agronomically important traits. Based on this promising work, there will likely be scope for quick improvement of this orphan crop through breeding.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

1. Damien Richard
2. Liam P Shaw
3. Rob Lanfear
4. Russell Corbett-Detig
5. Angie Hinrichs
6. Jakob McBroome
7. Yatish Turakhia
8. Mislav Acman
9. Christopher J Owen
10. Cedric CS Tan
11. Lucy van Dorp
12. François Balloux

Reviewed by ScreenIT