Genomics

DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants

1. Simon C Biddie
2. Giovanna Weykopf
3. Elizabeth F. Hird
4. Elias T. Friman
5. Wendy A Bickmore

Reviewed by Review Commons

An improved chromosome-level genome assembly of perennial ryegrass ( Lolium perenne L.)

1. Yutang Chen
2. Roland Kölliker
3. Martin Mascher
4. Dario Copetti
5. Axel Himmelbach
6. Nils Stein
7. Bruno Studer

• Curated by GigaByte

  Editors Assessment:

  This Data Release paper presents an updated genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss (Kyuss v2.0). To correct for structural the authors de novo assembled the genome again with ONT long-reads and generated 50-fold coverage high-throughput chromosome conformation capture (Hi-C) data to assist pseudo-chromosome construction. After being asked for some more improvements to gene and repeat annotation the authors now demonstrate the new assembly is more contiguous, more complete, and more accurate than Kyuss v1.0 and shows the correct pseudo-chromosome structure. This more accurate data have great potential for downstream genomic applications, such as read mapping, variant calling, genome-wide association studies, comparative genomics, and evolutionary biology. These future analyses being able to benefit forage and turf grass research and breeding.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Switching of RNA splicing regulators in immature neuroblasts during adult neurogenesis

1. Corentin Bernou
2. Marc-André Mouthon
3. Mathieu Daynac
4. Thierry Kortulewski
5. Benjamin Demaille
6. Vilma Barroca
7. Sebastien Couillard-Despres
8. Nathalie Dechamps
9. Véronique Ménard
10. Léa Bellenger
11. Christophe Antoniewski
12. Alexandra Déborah Chicheportiche
13. François Dominique Boussin

• Curated by eLife

  eLife assessment

  This useful manuscript presents an intriguing potential refinement of models for adult SVZ neurogenesis, and highlights the role of RNA splicing at specific stages in the lineage. Unfortunately, the evidence does not fully support the claims, leaving it currently incomplete. The proposed role of RNA splicing in neuronal differentiation, though interesting, remains unexplored and would benefit significantly from targeted gene manipulation studies.

Reviewed by eLife

NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

1. Luke Saville
2. Li Wu
3. Jemaneh Habtewold
4. Yubo Cheng
5. Babita Gollen
6. Liam Mitchell
7. Matthew Stuart-Edwards
8. Travis Haight
9. Majid Mohajerani
10. Athanasios Zovoilis

Reviewed by Review Commons

Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

1. Reese Richardson
2. Heliodoro Tejedor Navarro
3. Luis A Nunes Amaral
4. Thomas Stoeger

• Curated by eLife

  eLife assessment

  This study investigated the factors related to understudied genes in biomedical research. It showed that understudied genes are largely abandoned at the writing stage, and it identified a number of biological and experimental factors that influence which genes are selected for investigation. The study is an important contribution to this branch of meta-research, and the evidence in support of the findings is solid.

Reviewed by eLife

Structural variation discovery in wheat using PacBio high‐fidelity sequencing

1. Zhiliang Zhang
2. Jijin Zhang
3. Lipeng Kang
4. Xuebing Qiu
5. Song Xu
6. Jun Xu
7. Yafei Guo
8. Zelin Niu
9. Beirui Niu
10. Aoyue Bi
11. Xuebo Zhao
12. Daxing Xu
13. Jing Wang
14. Changbin Yin
15. Fei Lu

Reviewed by PREreview

Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations

1. Maria L Adelus
2. Jiacheng Ding
3. Binh T Tran
4. Austin C Conklin
5. Anna K Golebiewski
6. Lindsey K Stolze
7. Michael B Whalen
8. Darren A Cusanovich
9. Casey E Romanoski

• Curated by eLife

  eLife assessment

  This is a fundamental resource of snRNA-seq and and chromatin accessibility data from human aortic endothelial cells (ECs), treated with relevant perturbations such as IL1b, TGFB2, or si-EGR. The authors show that ECs can be categorized by distinct subpopulations of differing plasticity. The support for the existence of these subpopulations is compelling, supported also by three publicly available scRNA-seq datasets, and differential enrichment of coronary artery disease associated SNPs in open chromatin in these subpopulations.

Reviewed by eLife

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

1. Magnus Wolf
2. Bruno Lopes da Silva Ferrette
3. Raphael T. F. Coimbra
4. Menno de Jong
5. Marcel Nebenfuehr
6. David Prochotta
7. Yannis Schöneberg
8. Konstantin Zapf
9. Jessica Rosenbaum
10. Hannah A. Mc Intyre
11. Julia Maier
12. Clara C.S. de Souza
13. Lucas M. Gehlhaar
14. Melina J. Werner
15. Henrik Oechler
16. Marie Wittekind
17. Moritz Sonnewald
18. Maria A. Nilsson
19. Axel Janke
20. Sven Winter

• Curated by GigaByte

  Editors Assessment:

  The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.

  **This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

1. Joshua M. Kirsch
2. Andrew J. Hryckowian
3. Breck A. Duerkop

Reviewed by Arcadia Science

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

1. Mathieu Hénault
2. Souhir Marsit
3. Guillaume Charron
4. Christian R Landry

• Curated by eLife

  eLife assessment

  This valuable study advances our understanding of the forces that shape the genomic landscape of transposable elements. By exploiting both long-read sequencing of mutation accumulation lines and in vivo transposition assays, the authors offer compelling evidence that structural variation rather than transposition largely shapes transposable element copy number evolution in budding yeast. The work will be of interest to the transposable element and genome evolution communities.

Reviewed by eLife