Genomics

Copy number footprints of platinum-based anticancer therapies

1. Santiago Gonzalez
2. Nuria Lopez-Bigas
3. Abel Gonzalez-Perez

Reviewed by Review Commons

Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis

1. Sana Naderi
2. Peter E Chen
3. Carmen Lia Murall
4. Raphael Poujol
5. Susanne Kraemer
6. Bradley S Pickering
7. Selena M Sagan
8. B Jesse Shapiro

• Curated by eLife

  eLife assessment

  This important study offers compelling evidence, in the form of a rigorous and clear analysis of SARS-CoV-2 mutations observed within non-human animal hosts, of viral mutations that may provide an adaptive advantage within hosts. The authors could, however, improve the description of some elements of their methods and analysis approach, and they should cite additional relevant literature. The findings are relevant to those interested in the ecology of infectious disease, epidemiology, and specifically those who are interested in the genetic underpinnings of pandemic potential.

Reviewed by eLife

T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

1. Alexandro Landshammer
2. Adriano Bolondi
3. Helene Kretzmer
4. Christian Much
5. René Buschow
6. Alina Rose
7. Hua-Jun Wu
8. Sebastian D Mackowiak
9. Bjoern Braendl
10. Pay Giesselmann
11. Rosaria Tornisiello
12. Krishna Mohan Parsi
13. Jack Huey
14. Thorsten Mielke
15. David Meierhofer
16. René Maehr
17. Denes Hnisz
18. Franziska Michor
19. John L Rinn
20. Alexander Meissner

• Curated by eLife

  eLife assessment

  Based on a large set of complementary experiments, the authors propose that the lncRNA LNCSOX17 regulates human definitive endoderm differentiation, although its function is not related to the adjacent SOX17 gene in the same topological domain (TAD). The findings are important and supported by convincing data, although the molecular mechanism by which LNCSOX17 regulates endoderm differentiation stays unresolved.

Reviewed by eLife

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

1. Jean-Marc Aury
2. Stefan Engelen
3. Benjamin Istace
4. Cécile Monat
5. Pauline Lasserre-Zuber
6. Caroline Belser
7. Corinne Cruaud
8. Hélène Rimbert
9. Philippe Leroy
10. Sandrine Arribat
11. Isabelle Dufau
12. Arnaud Bellec
13. David Grimbichler
14. Nathan Papon
15. Etienne Paux
16. Marion Ranoux
17. Adriana Alberti
18. Patrick Wincker
19. Frédéric Choulet

Reviewed by GigaScience

The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae)

1. Audrey J. Majeske
2. Alejandro J. Mercado Capote
3. Aleksey Komissarov
4. Anna Bogdanova
5. Nikolaos V. Schizas
6. Stephanie O. Castro Márquez
7. Kenneth Hilkert
8. Walter Wolfsberger
9. Tarás K. Oleksyk

Reviewed by GigaByte

Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links

1. Nathan R Johnson
2. Luis F Larrondo
3. José M Álvarez
4. Elena A Vidal

• Curated by eLife

  eLife assessment

  This paper is of interest to scientists within the field of RNA silencing and evolution. The data analysis is rigorous, and the conclusions are justified by the data. The key claims of the manuscript provide a compelling approach to identifying and annotating microRNAs in fungi although there is a limitation in the functional validation of the identified miRNAs.

Reviewed by eLife

The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells

1. Keisuke Shoji
2. Yusuke Umemura
3. Susumu Katsuma
4. Yukihide Tomari

Reviewed by Review Commons

Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance

1. Fares Z Najar
2. Evan Linde
3. Chelsea L Murphy
4. Veniamin A Borin
5. Huan Wang
6. Shozeb Haider
7. Pratul K Agarwal

• Curated by eLife

  eLife assessment

  Najar et al., present a method for the identification of the emergence of new variants prior to the accompanying surge in cases by examining the trend of accumulated non-synonymous mutations from the original Wuhan 2020 SARS-CoV-2 strain. This is an interesting idea but requires additional evidence to establish this as a robust tool for predictions.

Reviewed by eLife

Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns

1. Simon Grund Sørensen
2. Amruta Shrikhande
3. Gustav Alexander Poulsgaard
4. Mikkel Hovden Christensen
5. Johanna Bertl
6. Britt Elmedal Laursen
7. Eva R Hoffmann
8. Jakob Skou Pedersen

• Curated by eLife

  eLife assessment

  This paper will be of interest to researchers in the field of genomic medicine and cancer mutagenesis. It presents predictive models with potential clinical applications that can identify patients with specific gene dysfunction based on characteristic patterns of mutation. The key findings are well supported.

Reviewed by eLife

Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project

1. Emmelien Vancaester
2. Mark Blaxter

Reviewed by Arcadia Science