Genomics

Interchromosomal segmental duplication drives translocation and loss of P. falciparum histidine-rich protein 3

1. Nicholas J Hathaway
2. Isaac E Kim
3. Neeva WernsmanYoung
4. Sin Ting Hui
5. Rebecca Crudale
6. Emily Y Liang
7. Christian P Nixon
8. David Giesbrecht
9. Jonathan J Juliano
10. Jonathan B Parr
11. Jeffrey A Bailey

• Curated by eLife

  eLife assessment

  This work provides important insight into the mechanisms of hrp2 and particularly hrp3 deletion generation. The generation of additional long-read data alongside a new analysis of 19,000 public short-read sequenced genomes makes this the most detailed investigation currently available on this topic, which has high public health importance and also basic biological interest. The revised version of the manuscript provides convincing evidence for the proposed mechanisms.

Reviewed by eLife

Genome-wide mapping of native co-localized G4s and R-loops in living cells

1. Ting Liu
2. Xing Shen
3. Yijia Ren
4. Hongyu Lu
5. Yu Liu
6. Chong Chen
7. Lin Yu
8. Zhihong Xue

• Curated by eLife

  eLife assessment

  This study describes a useful antibody-free method to map both G-quadruplexes and R-loops in vertebrate cells independently of the BG4 and S9.6 antibodies. It also reveals that the helicase Dhx9 can affect the self-renewal and differentiation capacities of mESCs, perhaps by regulating co-localized G4s and R-loops. The datasets provided might constitute a good starting point for future functional studies, and although the strength of the evidence that DHX9 interferes with the ability of mESCs to differentiate by regulating directly the stability of either G4s or R-loops has been improved compared to a previous version, it is still incomplete.

Reviewed by eLife

Regulatory genome annotation of 33 insect species

1. Hasiba Asma
2. Ellen Tieke
3. Kevin D Deem
4. Jabale Rahmat
5. Tiffany Dong
6. Xinbo Huang
7. Yoshinori Tomoyasu
8. Marc S Halfon

• Curated by eLife

  eLife assessment

  In the revised version of this important study, the authors present a convincing pipeline for insect genome regulatory annotation across 33 insect genomes spanning 5 orders. Despite technical limitations in the field owing to the lack of comprehensive knowledge of enhancer content in any system, the authors employ several independent downstream analyses to support the validity of their enhancer predictions for a subset of these genomes. Taken together, the revised results suggest that this prediction pipeline may have uses in identifying functional enhancers across large phylogenetic distances. Reviewers note caveats that an experimental validation is not yet available in the field to validate a large class of newly identified enhancers across such evolutionary distances, and other pipelines might be of use to compare. This work will be of interest to the computational genomics, evolutionary biology, and gene regulation fields.

Reviewed by eLife

Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling

1. Chen Weng
2. Jonathan S. Weissman
3. Vijay G. Sankaran

Reviewed by Arcadia Science

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

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

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

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