Genomics

A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

1. Weiwei Yang
2. Yu-Cheng Lin
3. William Johnson
4. Nan Dai
5. Romualdas Vaisvila
6. Peter Weigele
7. Yan-Jiun Lee
8. Ivan R Corrêa
9. Ira Schildkraut
10. Laurence Ettwiller

• Curated by eLife

  Evaluation Summary:

  This work will interest researchers who want to explore the functional potential in metagenomes. The authors present a new computational method, MetaGPA, for performing enrichment analysis on cohorts of metagenomes. They then use this approach to identify an enzyme that can modify cytosines in DNA from natural bacteriophage populations. Though successful, the approach needs to improve in clarity and methodology to be both reproducible and of broader impact, as claimed.

  (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

Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study

1. Sanjeet Kumar
2. Kanika Bansal

Reviewed by ScreenIT

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

1. Áine O’Toole
2. Oliver G. Pybus
3. Michael E. Abram
4. Elizabeth J. Kelly
5. Andrew Rambaut

Reviewed by ScreenIT

Comparative transcriptomic analysis reveals translationally relevant processes in mouse models of malaria

1. Athina Georgiadou
2. Claire Dunican
3. Pablo Soro-Barrio
4. Hyun Jae Lee
5. Myrsini Kaforou
6. Aubrey J Cunnington

• Curated by eLife

  Evaluation Summary:

  In this work, the authors use independent public datasets to perform an unbiased investigation of the similarities and differences of mouse models to human malarial disease using comparative transcriptomics. Whilst the data cannot convincingly identify which mouse models are best suited for studying specific human malaria phenotypes, the comparative analyses do indicate that these models reflect the broad diversity of human disease.

  (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 agreed to share their name with the authors.)

Reviewed by eLife

The whale shark genome reveals patterns of vertebrate gene family evolution

1. Milton Tan
2. Anthony K Redmond
3. Helen Dooley
4. Ryo Nozu
5. Keiichi Sato
6. Shigehiro Kuraku
7. Sergey Koren
8. Adam M Phillippy
9. Alistair DM Dove
10. Timothy Read

• Curated by eLife

  Evaluation Summary:

  This manuscript is of interest in the field of comparative genomics as it provides novel genomic resources for the whale shark, which belongs to a group of vertebrates which has to date limited available genomic data. While the strength of this manuscript is the publication of a novel genomic resource, the importance of the conclusions and the broader impact remain unclear, particularly because the work on its own does not yet provide new insights into the biology of whale sharks.

  (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

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

1. Ana Paula Muterle Varela
2. Janira Prichula
3. Fabiana Quoos Mayer
4. Richard Steiner Salvato
5. Fernando Hayashi Sant'Anna
6. Tatiana Schäffer Gregianini
7. Letícia Garay Martins
8. Adriana Seixas
9. Ana Beatriz Gorini da Veiga

Reviewed by ScreenIT

In vitro culture of freshly isolated Trypanosoma brucei brucei bloodstream forms results in gene copy-number changes

1. Julius Mulindwa
2. Geofrey Ssentamu
3. Enock Matovu
4. Kevin Kamanyi Marucha
5. Francisco Aresta-Branco
6. Claudia Helbig
7. Christine Clayton

Reviewed by Review Commons

Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories

1. DeElegant Robinson
2. Michael Place
3. James Hose
4. Adam Jochem
5. Audrey P Gasch

• Curated by eLife

  Evaluation Summary:

  This study investigates the effect of copy number variants across all genes in Saccharomyces cerevisiae, and the variation across different genetic backgrounds. Interestingly, apart from universal effects common to most of the genetic backgrounds, the authors also report strain-specific effects related to gene copy number variants.

  (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

High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021

1. Ueric José Borges de Souza
2. Raíssa Nunes dos Santos
3. Fabrício Souza Campos
4. Karine Lima Lourenço
5. Flavio Guimarães da Fonseca
6. Fernando Rosado Spilki
7. Corona-ômica.BR/MCTI Network

Reviewed by ScreenIT

SARS-CoV-2 genome sequencing with Oxford Nanopore Technology and Rapid PCR Barcoding in Bolivia

1. Oscar M. Rollano-Peñaloza
2. Carmen Delgado Barrera
3. Aneth Vasquez Michel

Reviewed by ScreenIT