1. Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

    This article has 8 authors:
    1. Yiming Xu
    2. Wanqiu Wang
    3. Jiefeng Huang
    4. Minjie Xu
    5. Binhu Wang
    6. Yingsong Wu
    7. Yongzhong Xie
    8. Jianbo Jian
    This article has been curated by 1 group:
    • 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  2. Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

    This article has 20 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  3. Cell type-specific immune regulation under symbiosis in a facultatively symbiotic coral

    This article has 11 authors:
    1. Maria Valadez-Ingersoll
    2. Hanny E. Rivera
    3. JK 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture

    This article has 10 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  5. Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

    This article has 9 authors:
    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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  6. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis

    This article has 7 authors:
    1. Caroline A. McCormick
    2. Stuart Akeson
    3. Sepideh Tavakoli
    4. Dylan Bloch
    5. Isabel N. Klink
    6. Miten Jain
    7. Sara H. Rouhanifard
    This article has been curated by 1 group:
    • 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  7. Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

    This article has 20 authors:
    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

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  8. Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

    This article has 7 authors:
    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

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  9. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

    This article has 14 authors:
    1. Rafael Moysés Alves
    2. Vinicius A. C. de Abreu
    3. Rafaely Pantoja Oliveira
    4. João Victor dos Anjos Almeida
    5. Mauro de Medeiros de Oliveira
    6. Saura R. Silva
    7. Alexandre R. Paschoal
    8. Sintia S. de Almeida
    9. Pedro A. F. de Souza
    10. Jesus A. Ferro
    11. Vitor F. O. Miranda
    12. Antonio Figueira
    13. Douglas S. Domingues
    14. Alessandro M. Varani

    Reviewed by GigaScience

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  10. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

    This article has 2 authors:
    1. Raehoon Jeong
    2. Martha L. Bulyk
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper addresses a question regarding the low overlap between genetic variants linked to human complex diseases and variants linked to differences in gene expression. Some of the analyses supporting the main claims are convincing, and the key conclusions are valuable and of interest to readers in the fields of human genetics and functional genomics. However, chromatin accessibility QTL (caQTL) also carry the limitation of not identifying the genes that directly mediate the influence on disease phenotypes.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
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