Genomics

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

1. Hong Kong Biodiversity Genomics Consortium
2. Jerome H.L. Hui
3. Ting Fung Chan
4. Leo L. Chan
5. Siu Gin Cheung
6. Chi Chiu Cheang
7. James K.H. Fang
8. Juan Diego Gaitan-Espitia
9. Stanley C.K. Lau
10. Yik Hei Sung
11. Chris K.C. Wong
12. Kevin Y.L. Yip
13. Yingying Wei
14. Wai Lok So
15. Wenyan Nong
16. Sean T.S. Law
17. Paul Crow
18. Aiko Leong
19. Liz Rose-Jeffreys
20. Ho Yin Yip

• Curated by GigaByte

  Editors Assessment: This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong (see https://doi.org/10.46471/GIGABYTE_SERIES_0006). This example assembles the genome of the black-faced spoonbill (Platalea minor), an emblematic wading bird from East Asia that is classified as globally endangered by the IUCN. This Data Release reporting a 1.24Gb chromosomal-level genome assembly produced using a combination of PacBio SMRT and Omni-C scaffolding technologies. BUSCO and Merqury validation were carried out, gene models created, and peer reviewers also requested MCscan synteny analysis. This showed the genome assembly had high sequence continuity with scaffold length N50=53 Mb. Presenting data from 14 individuals this will hopefully be a useful and valuable resources for future population genomic studies aimed at better understanding spoonbill species numbers and conservation.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Single-cell RNA-sequencing reveals immune system compartmentalization under symbiosis in the stony coral Oculina arbuscula

1. Maria Valadez-Ingersoll
2. Hanny E. Rivera
3. Jeric Da-Anoy
4. Matthew R. Kanke
5. Kelly Gomez-Campo
6. M. Isabel Martinez-Rugerio
7. Julian Kwan
8. Ryan Hekman
9. Andrew Emili
10. Thomas D. Gilmore
11. Sarah W. Davies

Reviewed by Arcadia Science

A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture

1. Teresa Attenborough
2. Kate A Rawlinson
3. Carmen L Diaz Soria
4. Kirsty Ambridge
5. Geetha Sankaranarayanan
6. Jennie Graham
7. James A Cotton
8. Stephen R Doyle
9. Gabriel Rinaldi
10. Matthew Berriman

• Curated by eLife

  eLife assessment

  This is a valuable study in which the authors provide an expression profile of the human blood fluke, Schistosoma mansoni. A strength of this solid study is in its inclusion of in situ hybridisation to validate the predictions of the transcript analysis.

Reviewed by eLife

Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

1. Omid Gholamalamdari
2. Tom van Schaik
3. Yuchuan Wang
4. Pradeep Kumar
5. Liguo Zhang
6. Yang Zhang
7. Gabriela A. Hernandez Gonzalez
8. Athanasios E. Vouzas
9. Peiyao A. Zhao
10. David M. Gilbert
11. Jian Ma
12. Bas van Steensel
13. Andrew S. Belmont

• Curated by eLife

  eLife assessment

  This is a valuable manuscript that successfully integrates several datasets to determine genome interactions with several nuclear bodies. The integrative datasets are a major strength of the manuscript. The evidence supporting the central claims is varied in its strength ranging from solid to incomplete. Orthogonal evidence validating the novel methodologies with alternative approaches would better support the central claims. We encourage the authors to consider a revised manuscript which addresses these points.

Reviewed by eLife

Tradeoffs in Modeling Context Dependency in Complex Trait Genetics

1. Eric Weine
2. Samuel Pattillo Smith
3. Rebecca Kathryn Knowlton
4. Arbel Harpak

• Curated by eLife

  eLife assessment

  The study presents a framework viewing gene-by-environment (GxE) effect estimation as a bias-variance tradeoff problem. The authors convincingly show that greater statistical power can be achieved in detecting GxE if an underlying model of polygenic GxE is assumed. This polygenic amplification model is a truly novel view with fundamental promise for the detection of GxE in genomic datasets. That said, at present the polygenic architecture investigation presented in the manuscript is somewhat limited to specific models and may not adequately build over the bias-variance tradeoff part of the manuscript. If the authors can show in their simulations that they can in principle detect more complex scenarios of amplification, then the strength of the paper would be enhanced.

Reviewed by eLife

Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

1. Abhishek Dutta
2. Fabien Dutreux
3. Marion Garin
4. Claudia Caradec
5. Anne Friedrich
6. Gauthier Brach
7. Pia Thiele
8. Bertrand Llorente
9. Joseph Schacherer

Reviewed by Review Commons

Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis

1. Caroline A. McCormick
2. Stuart Akeson
3. Sepideh Tavakoli
4. Dylan Bloch
5. Isabel N. Klink
6. Miten Jain
7. Sara H. Rouhanifard

• Curated by GigaByte

  Editors Assessment:

  Oxford nanopore direct RNA sequencing (DRS) is a relatively new sequencing technology enabling measurements of RNA modifications. In vitro transcription (IVT)-based negative controls (i.e. modification-free transcripts) are a practical and targeted control for this direct sequencing, providing a baseline measurement for canonical nucleotides within a matched and biologically-derived sequence context. This work presents exactly this type of a long-read, multicellular, poly-A RNA-based, IVT-derived, unmodified transcriptome dataset. Review flagging more statistical analyses needed be performed for the data quality, and this was provided. The resulting data providing a resource to the direct RNA analysis community, helping reduce the need for expensive IVT library preparation and sequencing for human samples. And also serving as a framework for RNA modification analysis in other organisms.

  This evaluation refers to version 1 and 2 of the preprint

Reviewed by GigaByte

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

1. Nikolai Hecker
2. Niklas Kempynck
3. David Mauduit
4. Darina Abaffyová
5. Roel Vandepoel
6. Sam Dieltiens
7. Ioannis Sarropoulos
8. Carmen Bravo González-Blas
9. Elke Leysen
10. Rani Moors
11. Gert Hulselmans
12. Lynette Lim
13. Joris De Wit
14. Valerie Christiaens
15. Suresh Poovathingal
16. Stein Aerts

Reviewed by preLights

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

1. Kira Breunig
2. Xiufen Lei
3. Mauro Montalbano
4. Gabriela D. A. Guardia
5. Shiva Ostadrahimi
6. Victoria Alers
7. Adam Kosti
8. Jennifer Chiou
9. Nicole Klein
10. Corina Vinarov
11. Lily Wang
12. Mujia Li
13. Weidan Song
14. W. Lee Kraus
15. David S. Libich
16. Stefano Tiziani
17. Susan T. Weintraub
18. Pedro A. F. Galante
19. Luiz O. F. Penalva

• Curated by eLife

  eLife assessment

  This study reports valuable insights into the interactome of the RNA-binding protein SERBP1 and possible links through PARylation to a diverse set of processes including splicing, cell division, and ribosome biogenesis. The diversity of processes SERBP1 may regulate means this work would be of very broad interest to the cell biology community. However, whereas the proteomics data are solid, the functional connection to downstream processes and the link to Alzheimer's disease are still incomplete, as they rely on a very limited set of experiments and patient samples.

Reviewed by eLife

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

1. Scott Ferguson
2. Ashley Jones
3. Kevin Murray
4. Rose L. Andrew
5. Helen Bothwell
6. Benjamin Schwessinger
7. Justin Borevitz

Reviewed by GigaScience