Genomics

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

Cell type-specific immune regulation under symbiosis in a facultatively symbiotic coral

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. Sebastian Metz
8. Michael Sweet
9. Julian Kwan
10. Ryan Hekman
11. Andrew Emili
12. Thomas D Gilmore
13. 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

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. Lars Borm
8. Ioannis Sarropoulos
9. Carmen Bravo González-Blas
10. Julie De Man
11. Kristofer Davie
12. Elke Leysen
13. Jeroen Vandensteen
14. Rani Moors
15. Gert Hulselmans
16. Lynette Lim
17. Joris De Wit
18. Valerie Christiaens
19. Suresh Poovathingal
20. Stein Aerts

Reviewed by preLights

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