Genomics

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

1. André Gomes-dos-Santos
2. Manuel Lopes-Lima
3. André M. Machado
4. Thomas Forest
5. Guillaume Achaz
6. Amílcar Teixeira
7. Vincent Prié
8. L. Filipe C. Castro
9. Elsa Froufe

• Curated by GigaByte

  Editor’s Assessment

  Like other mollusc species, the freshwater pearl mussel (Margaritifera margaritifera) has a challenging genome to assemble owing to the large size of their genomes, heterozygosity, and repetitive sequence. The first published M. margaritifera genome was highly fragmented, but here an improved reference genome assembly was generated using PacBio CLR long reads to reduce fragmentation levels, missing and truncated genes, and chimerically assembled regions. The number of gene models predicted is a bit higher compared than other molluscan genomes, but after clarification and double checking these seem in line with some Mollusca and Bivalvia with similar and higher numbers of gene predictions. This new genome represents a new resource to start exploring the many biological, ecological, and evolutionary features of this threatened and commercially important group of organisms.

  This assessment refers to version 1 of this preprint.

Reviewed by GigaByte

Annotating Metagenomically Assembled Bacteriophage from a Unique Ecological System using Protein Structure Prediction and Structure Homology Search

1. Henry Say
2. Ben Joris
3. Daniel Giguere
4. Gregory B. Gloor

Reviewed by Arcadia Science

Genome dynamics across the evolutionary transition to endosymbiosis

1. Stefanos Siozios
2. Pol Nadal-Jimenez
3. Tal Azagi
4. Hein Sprong
5. Crystal L. Frost
6. Steven R. Parratt
7. Graeme Taylor
8. Laura Brettell
9. Kwee Chin Liew
10. Larry Croft
11. Kayla C. King
12. Michael A. Brockhurst
13. Václav Hypša
14. Eva Novakova
15. Alistair C. Darby
16. Gregory D.D. Hurst

Reviewed by Arcadia Science

Histone variants shape chromatin states in Arabidopsis

1. Bhagyshree Jamge
2. Zdravko J Lorković
3. Elin Axelsson
4. Akihisa Osakabe
5. Vikas Shukla
6. Ramesh Yelagandula
7. Svetlana Akimcheva
8. Annika Luisa Kuehn
9. Frédéric Berger

• Curated by eLife

  eLife assessment

  This study presents an important description on the dynamics of histone variant exchange controlling the organization of the chromatin state of the Arabidopsis genome, combining the analysis of histone variants, histone modification, and chromatin states. The evidence supporting the claims of the authors is compelling. This work will be of great interest to those in the field of epigenetics and chromatin biology.

Reviewed by eLife

Tau polarizes an aging transcriptional signature to excitatory neurons and glia

1. Timothy Wu
2. Jennifer M Deger
3. Hui Ye
4. Caiwei Guo
5. Justin Dhindsa
6. Brandon T Pekarek
7. Rami Al-Ouran
8. Zhandong Liu
9. Ismael Al-Ramahi
10. Juan Botas
11. Joshua M Shulman

• Curated by eLife

  eLife assessment

  This is an important study that defines cell type changes upon the expression of a mutant tau protein and put it into context of human postmortem tissue. Technically, the single cell mRNA sequencing data are convincing but the loss of neurons already at the earliest stages assessed in this model may rather suggest there are also elements of developmental toxicity.

Reviewed by eLife

Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning

1. Gemma E May
2. Christina Akirtava
3. Matthew Agar-Johnson
4. Jelena Micic
5. John Woolford
6. Joel McManus

• Curated by eLife

  eLife assessment

  Protein abundance is the result of many layers of regulation, including at the levels of transcription, mRNA stability, translation and protein degradation. Many transcripts contain short upstream ORFs (uORFS), but their effects on the translation of the main ORFs are difficult to predict as they are sometimes negative, positive and of different magnitudes. Here, the authors identify features of uORFs using massively parallel reporter assays, and these features help predict uORF effects on translation of main ORFs. The results will be an important resource for the community of researchers using this model organism and for the molecular and cell biology community in general as they allow to better understand how genes are regulated. There are also areas in which the authors' claims or conclusions are not fully justified and require either additional statistical analysis or new experimentation.

Reviewed by eLife

Multi-omics analysis identifies LBX1 and NHLH1 as central regulators of human midbrain dopaminergic neuron differentiation

1. Borja Gomez Ramos
2. Jochen Ohnmacht
3. Nikola de Lange
4. Aurélien Ginolhac
5. Elena Valceschini
6. Aleksandar Rakovic
7. Rashi Halder
8. François Massart
9. Christine Klein
10. Roland Krause
11. Marcel H. Schulz
12. Thomas Sauter
13. Rejko Krüger
14. Lasse Sinkkonen

Reviewed by Review Commons

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

1. J. William O. Ballard
2. Matt A. Field
3. Richard J. Edwards
4. Laura A.B. Wilson
5. Loukas G. Koungoulos
6. Benjamin D. Rosen
7. Barry Chernoff
8. Olga Dudchenko
9. Arina Omer
10. Jens Keilwagen
11. Ksenia Skvortsova
12. Ozren Bogdanovic
13. Eva Chan
14. Robert Zammit
15. Vanessa Hayes
16. Erez Lieberman Aiden

Reviewed by GigaScience

The mutational signatures of poor treatment outcomes on the drug-susceptible Mycobacterium tuberculosis genome

1. Yiwang Chen
2. Qi Jiang
3. Mijiti Peierdun
4. Howard E Takiff
5. Qian Gao

• Curated by eLife

  eLife assessment

  In this useful study, a GWAS-type analysis is applied to clinical Mycobacterium tuberculosis isolates to discover genetic polymorphisms linked to poor tuberculosis outcomes. The evidence for the detected associations is still incomplete, as the corresponding polymorphisms are not adequate to power a prediction model for infection outcome, although key host factors - including patient age, sex, and duration of diagnostic delay (which have stronger predictive value) - appear to enhance predictive capacity.

Reviewed by eLife

Genome assembly of the deep-sea coral Lophelia pertusa

1. Santiago Herrera
2. Erik E. Cordes

Reviewed by GigaByte