Genomics

Essentiality and dynamic expression of the human tRNA pool during viral infection

1. Noa Aharon-Hefetz
2. Michal Schwartz
3. Orna Dahan
4. Noam Stern-Ginossar
5. Yitzhak Pilpel

Reviewed by Review Commons

Dynamics and Regulatory Roles of RNA m6A Methylation in Unbalanced Genomes

1. Shuai Zhang
2. Xinyu Liu
3. Ruixue Wang
4. Junhan Wang
5. Ludan Zhang
6. Lin Sun

• Curated by eLife

  eLife assessment

  This valuable study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, using aneuploid Drosophila as a model, and suggests that the dosage compensation complex and m6A act in a feedback loop. The evidence is incomplete due to technical concerns, as quantitative assessments are being made using non-quantitative methods, and the study would be improved by further functional studies. If strengthened, the study will be of interest to RNA and developmental biologists.

Reviewed by eLife

Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow

1. Sila Gerlevik
2. Nogayhan Seymen
3. Shan Hama
4. Warisha Mumtaz
5. I Richard Thompson
6. Seyed R Jalili
7. Deniz E Kaya
8. Alfredo Iacoangeli
9. Andrea Pellagatti
10. Jacqueline Boultwood
11. Giorgio Napolitani
12. Ghulam J Mufti
13. Mohammad M Karimi

• Curated by eLife

  eLife assessment

  This manuscript uses public datasets of myelodysplastic syndrome (MDS) patients to undertake a multi-omics analysis of clinical, genomic, and transcriptomic datasets. Useful findings are provided by way of interesting correlations of specific mutations with inflammation and differing clinical outcomes. The evidence is solid and interesting, and the manuscript is of substantive value to hematologists and clinical immunologists.

Reviewed by eLife

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

1. Mehul Vora
2. Jonathan Dietz
3. Zachary Wing
4. Jun Liu
5. Christopher Rongo
6. Cathy Savage-Dunn

• Curated by eLife

  eLife assessment

  This study presents valuable findings that will allow for a better understanding of the targets of SMAD and Schnurri, transcription factors that act downstream in the BMP signalling pathway. The evidence presented in this manuscript is solid, but because the claims of a SMA-3/SMA-9 complex are not experimentally supported, they should be toned down. Revising the discussion to give a broader context of BMP-driven body size control would help the readers put this work in a larger context. This work will be of broad interest to colleagues studying BMP signalling across phyla.

Reviewed by eLife

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

1. Lenore Pipes
2. Rasmus Nielsen

• Curated by eLife

  eLife assessment

  This potentially important work presents a tool for performing phylogenetic taxonomic classification of DNA sequences. In terms of methodology, the work is compelling. The authors perform a benchmark experiment against current state-of-the-art tools using real and simulated datasets to demonstrate where the novel tool stands in the context of existing methods. However, the experimentation is still incomplete. It would benefit from a more thorough exploration of existing methods as well as data sets that better represent real-world use cases.

Reviewed by eLife

Expression of Most Retrotransposons in Human Blood Correlates with Biological Aging

1. Yi-Ting Tsai
2. Nogayhan Seymen
3. I Richard Thompson
4. Xinchen Zou
5. Warisha Mumtaz
6. Sila Gerlevik
7. Ghulam J Mufti
8. Mohammad M Karimi

• Curated by eLife

  eLife assessment

  Using multiple public datasets, this study investigates associations between retrotransposon element expression and methylation with age and inflammation. The study is valuable because a systematic analysis of retrotransposon element expression during human aging has been lacking, but the provided data must be considered incomplete due to the sole reliance on microarray expression data for the core analyses.

Reviewed by eLife

From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

1. Shaohua Gu
2. Yuanzhe Shao
3. Karoline Rehm
4. Laurent Bigler
5. Di Zhang
6. Ruolin He
7. Ruichen Xu
8. Jiqi Shao
9. Alexandre Jousset
10. Ville-Petri Friman
11. Xiaoying Bian
12. Zhong Wei
13. Rolf Kümmerli
14. Zhiyuan Li

• Curated by eLife

  eLife assessment

  This important study presents a novel pipeline for the large-scale genomic prediction of members of the non-ribosomal peptide group of pyoverdines based on a dataset from nearly 2000 Pseudomonas genomes. The advance presented in this study is based on convincing evidence. This study of bacterial siderophores has broad theoretical and practical implications beyond a singular subfield.

Reviewed by eLife

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

1. Yiming Xu
2. Wanqiu Wang
3. Jiefeng Huang
4. Minjie Xu
5. Binhu Wang
6. Yingsong Wu
7. Yongzhong Xie
8. Jianbo Jian

• Curated by GigaByte

  Editors Assessment:

  RAD-Seq (Restriction-site-associated DNA sequencing) is a cost-effective method for single nucleotide polymorphism (SNP) discovery and genotyping. In this study the authors performed a kinship analysis and pedigree reconstruction for two different cattle breeds (Angus and Xiangxi yellow cattle). A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping using RAD-Seq. Producing a SNP panel with 7305 SNPs capturing the maximum difference between paternal and maternal genome information, and being able to distinguish between the F1 and F2 generation with 90% accuracy. Peer review helped highlight better the practical applications of this work. The combination of the efficiency of RNA-seq and advances in kinship analysis here can helpfully help improve breed management, local resource utilization, and conservation of livestock.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

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