Genomics

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

Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

1. Héctor Castillo
2. Francisco Godoy
3. Clément Gilbert
4. Felipe Aguilera
5. Salvatore Spicuglia
6. Sylvain Marcellini

Reviewed by Review Commons

DNA methylation-environment interactions in the human genome

1. Rachel A Johnston
2. Katherine A Aracena
3. Luis B Barreiro
4. Amanda J Lea
5. Jenny Tung

• Curated by eLife

  eLife assessment

  This important paper uses a genome-wide, massively parallel reporter assay to determine how CpG methylation affects regulatory sequences that control the expression of human genes. The authors provide compelling evidence that methylation not only influences baseline activity of regulatory sequences but also the magnitude of acute responses to environmental stimuli. The findings are of broad interest, and the extensive data set will likely become a key resource for the community.

Reviewed by eLife

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

1. Stephanie H Chen
2. Alyssa M Martino
3. Zhenyan Luo
4. Benjamin Schwessinger
5. Ashley Jones
6. Tamene Tolessa
7. Jason G Bragg
8. Peri A Tobias
9. Richard J Edwards

Reviewed by GigaScience

Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

1. Mohammed Seba
2. Frederic Boccard
3. Stéphane Duigou

• Curated by eLife

  eLife assessment

  This important work combines DNA contact analysis and controlled genome rearrangements to investigate the processes that organize the E. coli chromosome, with a particular focus on how the SMC-related complex MukBEF is regulated. The evidence supporting the conclusions is compelling, with time-resolved experiments and analysis of mutant strains. The work will be of broad interest to chromosome biologists and bacterial cell biologists.

Reviewed by eLife

Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap

1. Mengxue Tian
2. Zhenjia Wang
3. Zhangli Su
4. Etsuko Shibata
5. Yoshiyuki Shibata
6. Anindya Dutta
7. Chongzhi Zang

• Curated by eLife

  eLife assessment

  The paper addresses the mechanism of initiation of DNA replication in human cells by analyzing published data on the location of origins of DNA replication and the location of binding sites in the genome for ORC and MCM2-7 complexes. There are some useful analyses of existing data but there are concerns regarding the conclusion that there might be alternative mechanisms for determining the location of origins of DNA replication in human cells compared to the well known mechanism known from many eukaryotic systems, including yeast, Xenopus, C. elegans and Drosophila. The lack of overlap between binding sites for ORC1 and ORC2, which are known to form a complex in human cells, is a particular concern and points to the evidence for the accurate localization of their binding sites in the genome being incomplete.

Reviewed by eLife