Searching journal content for articles similar to Bihoreau et al. 7 (5): 434.

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  1. Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
    • Basanta Bista,
    • Laura González-Rodelas,
    • Lucía Álvarez-González,
    • Zhi-qiang Wu,
    • Eugenia E. Montiel,
    • Ling Sze Lee,
    • Daleen B. Badenhorst,
    • Srihari Radhakrishnan,
    • Robert Literman,
    • Beatriz Navarro-Dominguez,
    • John B. Iverson,
    • Simon Orozco-Arias,
    • Josefa González,
    • Aurora Ruiz-Herrera,
    • and Nicole Valenzuela
    Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
    ....e., their haploid number, n), contain 98% and 99% of the assembly. The species-specific RNA-seq reads from multiple tissues used for annotation mapped to the assemblies at a rate of 97.3% for Apalone (using available transcriptomic data from blood, liver, ovary, and testis), and 96.1% for Staurotypus (using...
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  2. Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
    • Paige A. Byerly,
    • Alina von Thaden,
    • Evgeny Leushkin,
    • Leon Hilgers,
    • Shenglin Liu,
    • Sven Winter,
    • Tilman Schell,
    • Charlotte Gerheim,
    • Alexander Ben Hamadou,
    • Carola Greve,
    • Christian Betz,
    • Hanno J. Bolz,
    • Sven Büchner,
    • Johannes Lang,
    • Holger Meinig,
    • Evax Marie Famira-Parcsetich,
    • Sarah P. Stubbe,
    • Alice Mouton,
    • Sandro Bertolino,
    • Goedele Verbeylen,
    • Thomas Briner,
    • Lídia Freixas,
    • Lorenzo Vinciguerra,
    • Sarah A. Mueller,
    • Carsten Nowak,
    • and Michael Hiller
    Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
    ...are contained in chromosome-level scaffolds. These metrics exceed the standards set by the Vertebrate Genome Project (Rhie et al. 2021).View larger version: In this window In a new window Figure 1. Contiguity and Hi-C maps of both haplotype assemblies. (A,B) Visualization of contig (A) and scaffold (B) sizes...
  3. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    ...for the ancient human introduction to Orkney (Fig. 1A; Martínková et al. 2013; Wang et al. 2023). We refer to the latter samples in the following as continental voles. We used three M. obscurus voles as an outgroup. The average mapping depth was 26×, ranging from 17× to 41× per individual. After filtering, 23...
  4. Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
    • Peter Orchard,
    • Nandini Manickam,
    • Christa Ventresca,
    • Swarooparani Vadlamudi,
    • Arushi Varshney,
    • Vivek Rai,
    • Jeremy Kaplan,
    • Claudia Lalancette,
    • Karen L. Mohlke,
    • Katherine Gallagher,
    • Charles F. Burant,
    • and Stephen C.J. Parker
    Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
    ...different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell–specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform...
  5. Research: Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia
    • Emily E. Puckett and
    • Jason Munshi-South
    Genome Res. May 2019 29: 762-770; Published in Advance March 25, 2019, doi:10.1101/gr.235754.118
    ...and then sorted and indexed in SAMtools. All 54 s were also mapped to the Rnor_6 reference with Bowtie 2, sorted, and indexed and then had a set of 32,127 SNPs extracted using a position list and the mpileup function in SAMtools to make the data comparable to genotypes from 326 brown rats collected from around...
  6. Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
    • Kaitlin U. Laverty,
    • Jake M. Stout,
    • Mitchell J. Sullivan,
    • Hardik Shah,
    • Navdeep Gill,
    • Larry Holbrook,
    • Gintaras Deikus,
    • Robert Sebra,
    • Timothy R. Hughes,
    • Jonathan E. Page,
    • and Harm van Bakel
    Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
    ...analysis. To generate a genetic linkage map, we employed the SOILoCo pipeline, created by Scaglione et al. (2016) to create a map of the artichoke . We applied the pipeline to F1 data from a cross between a PK female and FN male. SOILoCo requires phasing of the parental scaffolds into blocks in which...
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  7. Research: Natural variation of histone modification and its impact on gene expression in the rat genome
    • Carola Rintisch,
    • Matthias Heinig,
    • Anja Bauerfeind,
    • Sebastian Schafer,
    • Christin Mieth,
    • Giannino Patone,
    • Oliver Hummel,
    • Wei Chen,
    • Stuart Cook,
    • Edwin Cuppen,
    • Maria Colomé-Tatché,
    • Frank Johannes,
    • Ritsert C. Jansen,
    • Helen Neil,
    • Michel Werner,
    • Michal Pravenec,
    • Martin Vingron,
    • and Norbert Hubner
    Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
    ...the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences...
  8. Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
    • Ian T. Fiddes,
    • Joel Armstrong,
    • Mark Diekhans,
    • Stefanie Nachtweide,
    • Zev N. Kronenberg,
    • Jason G. Underwood,
    • David Gordon,
    • Dent Earl,
    • Thomas Keane,
    • Evan E. Eichler,
    • David Haussler,
    • Mario Stanke,
    • and Benedict Paten
    Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
    ...mappings, naming each equivalence class of orthologs based upon an initial reference annotation, and add to this sets of newly discovered genes. This can provide valuable evolutionary insights. For example, the analysis of the rat shows that many of the alternative isoforms and projected transcription...
  9. RESOURCE: A Consensus Linkage Map of the Chicken Genome
    • Martien A.M. Groenen,
    • Hans H. Cheng,
    • Nat Bumstead,
    • Bernard F. Benkel,
    • W. Elwood Briles,
    • Terry Burke,
    • Dave W. Burt,
    • Lyman B. Crittenden,
    • Jerry Dodgson,
    • Jossi Hillel,
    • Sue Lamont,
    • Abel Ponce de Leon,
    • Morris Soller,
    • Hideaki Takahashi,
    • and Alain Vignal
    Genome Res. January 1, 2000 10: 137-147; doi:10.1101/gr.10.1.137
    ...A Consensus Linkage Map of the Chicken Genome Martien A.M. Groenen 1 , 15 , Hans H. Cheng 2 , Nat Bumstead 3 , Bernard F. Benkel 4 , W. Elwood Briles 5 , Terry Burke 6 , Dave W. Burt 7 , Lyman B. Crittenden 8...
  10. Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
    • Santosh S. Atanur,
    • İnanç Birol,
    • Victor Guryev,
    • Martin Hirst,
    • Oliver Hummel,
    • Catherine Morrissey,
    • Jacques Behmoaras,
    • Xose M. Fernandez-Suarez,
    • Michelle D. Johnson,
    • William M. McLaren,
    • Giannino Patone,
    • Enrico Petretto,
    • Charles Plessy,
    • Kathleen S. Rockland,
    • Charles Rockland,
    • Kathrin Saar,
    • Yongjun Zhao,
    • Piero Carninci,
    • Paul Flicek,
    • Ted Kurtz,
    • Edwin Cuppen,
    • Michal Pravenec,
    • Norbert Hubner,
    • Steven J.M. Jones,
    • Ewan Birney,
    • and Timothy J. Aitman
    Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
    .... Abstract The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina...
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