Genomics

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies

1. Miguel A. Naranjo-Ortiz
2. Manu Molina
3. Verónica Mixão
4. Toni Gabaldón

Reviewed by GigaScience

A curated human cellular microRNAome based on 196 primary cell types

1. Arun H. Patil
2. Andrea Baran
3. Zachary P. Brehm
4. Matthew N. McCall
5. Marc K. Halushka

Reviewed by GigaScience

The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging

1. Monica Sanchez-Contreras
2. Mariya T Sweetwyne
3. Kristine A Tsantilas
4. Jeremy A Whitson
5. Matthew D Campbell
6. Brenden F Kohrn
7. Hyeon Jeong Kim
8. Michael J Hipp
9. Jeanne Fredrickson
10. Megan M Nguyen
11. James B Hurley
12. David J Marcinek
13. Peter S Rabinovitch
14. Scott R Kennedy

• Curated by eLife

  eLife assessment

  The analysis of 89,000 independent somatic mtDNA mutations provides compelling evidence that allows the authors to refute the idea that reactive oxygen species (ROS) are a main driver of mtDNA mutagenesis, although ROS effects may still be tissue-dependent. These are fundamental results with convincing evidence, and they should appeal to a broad audience. The discovery of transversion mutations (C>A/G>T and C>G/G>C), which previously were assumed to be almost nonexistent, will nevertheless require additional validation.

Reviewed by eLife

Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration

1. Caetano Souto-Maior
2. Yazmin L. Serrano Negron
3. Susan T. Harbison

Reviewed by Review Commons

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