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A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection

https://doi.org/10.1101/668384
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Karyotypes and cellular DNA contents of three species of the subfamily Clupeinae
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
inferredcites →https://doi.org/10.1016/j.cub.2014.01.056openalex-snapshot
Supergenes and Complex Phenotypes
inferredcites →https://doi.org/10.1016/j.cub.2015.11.069openalex-snapshot
Divergence and Functional Degradation of a Sex Chromosome-like Supergene
inferredcites →https://doi.org/10.1016/j.fertnstert.2016.10.013openalex-snapshot
Translocations, inversions and other chromosome rearrangements
inferredcites →https://doi.org/10.1016/j.tig.2005.09.009openalex-snapshot
Chromosome evolution in eukaryotes: a multi-kingdom perspective
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/hdy.1984.127openalex-snapshot
Lack of correspondence between genetic and morphologic variability patterns in Atlantic herring (Clupea harengus)
inferredcites →https://doi.org/10.1038/hdy.2009.98openalex-snapshot
Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters
inferredcites →https://doi.org/10.1038/hdy.2017.54openalex-snapshot
Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
inferredcites →https://doi.org/10.1038/nature11832openalex-snapshot
A Y-like social chromosome causes alternative colony organization in fire ants
inferredcites →https://doi.org/10.1038/ng.3430openalex-snapshot
Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
inferredcites →https://doi.org/10.1038/ng.3443openalex-snapshot
A supergene determines highly divergent male reproductive morphs in the ruff
inferredcites →https://doi.org/10.1038/nmeth.1363openalex-snapshot
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/s41467-017-01370-1openalex-snapshot
Tracing the origin and evolution of supergene mimicry in butterflies
inferredcites →https://doi.org/10.1038/s41467-017-01982-7openalex-snapshot
Centromere evolution and CpG methylation during vertebrate speciation
inferredcites →https://doi.org/10.1073/pnas.1216128109openalex-snapshot
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
inferredcites →https://doi.org/10.1073/pnas.1617728114openalex-snapshot
Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean
inferredcites →https://doi.org/10.1086/521987openalex-snapshot
Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btm108openalex-snapshot
GenABEL: an R library for genome-wide association analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btq102openalex-snapshot
Genome-wide synteny through highly sensitive sequence alignment: Satsuma
inferredcites →https://doi.org/10.1093/bioinformatics/btt509openalex-snapshot
Infernal 1.1: 100-fold faster RNA homology searches
inferredcites →https://doi.org/10.1093/bioinformatics/btt563openalex-snapshot
Lep-MAP: fast and accurate linkage map construction for large SNP datasets
inferredcites →https://doi.org/10.1093/database/baw093openalex-snapshot
The Ensembl gene annotation system
inferredcites →https://doi.org/10.1093/genetics/23.1.28openalex-snapshot
INVERSIONS IN THE CHROMOSOMES OF DROSOPHILA PSEUDOOBSCURA
inferredcites →https://doi.org/10.1093/icesjms/fss038openalex-snapshot
Thermal windows supporting survival of the earliest life stages of Baltic herring (Clupea harengus)
inferredcites →https://doi.org/10.1093/icesjms/fsv103openalex-snapshot
Female ovarian abnormalities and reproductive failure of autumn-spawning herring (Clupea harengus membras) in the Baltic Sea
inferredcites →https://doi.org/10.1093/jhered/esx058openalex-snapshot
Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly
inferredcites →https://doi.org/10.1093/nar/gkn188openalex-snapshot
The Vienna RNA Websuite
inferredcites →https://doi.org/10.1093/nar/gkx1038openalex-snapshot
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot
UniProt: a worldwide hub of protein knowledge
inferredcites →https://doi.org/10.1093/nar/gky1141openalex-snapshot
miRBase: from microRNA sequences to function
inferredcites →https://doi.org/10.1101/gr.6386707openalex-snapshot
Recombination rate estimation in the presence of hotspots
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05639.xopenalex-snapshot
Environmental selection on transcriptome‐derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)
inferredcites →https://doi.org/10.1111/j.1601-5223.1981.tb01330.xopenalex-snapshot
Genetic variability in Atlantic herring (Clupea harengus harengus): description of protein loci and population data
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
inferredcites →https://doi.org/10.1158/0008-5472.can-17-0337openalex-snapshot
Variant Review with the Integrative Genomics Viewer
inferredcites →https://doi.org/10.1186/s12859-018-2485-7openalex-snapshot
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
inferredcites →https://doi.org/10.1371/journal.pbio.1001091openalex-snapshot
Modernizing Reference Genome Assemblies
inferredcites →https://doi.org/10.1371/journal.pgen.1000512openalex-snapshot
Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens
inferredcites →https://doi.org/10.1371/journal.pgen.1002412openalex-snapshot
A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken
inferredcites →https://doi.org/10.1371/journal.pgen.1002775openalex-snapshot
The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility
inferredcites →https://doi.org/10.1371/journal.pone.0102089openalex-snapshot
The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1371/journal.pone.0169087openalex-snapshot
The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
inferredcites →https://doi.org/10.1534/g3.111.000190openalex-snapshot
An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci
inferredcites →https://doi.org/10.1534/genetics.114.164293openalex-snapshot
A RAD-Tag Genetic Map for the Platyfish ( Xiphophorus maculatus ) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.48550/arxiv.1605.04619openalex-snapshot
An end-to-end assembly of the Aedes aegypti genome
inferredcites →https://doi.org/10.7554/elife.12081openalex-snapshot
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
inferredcites →https://doi.org/10.7554/elife.23907openalex-snapshot
Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jas.2022.105703openalex-snapshot
Ancient DNA sequence quality is independent of fish bone weight
inferred← citeshttps://doi.org/10.1038/s41598-019-54151-9openalex-snapshot
Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly
inferred← citeshttps://doi.org/10.1093/jhered/esaa020openalex-snapshot
Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change
inferred← citeshttps://doi.org/10.1101/2022.05.18.492457openalex-snapshot
Serial depletion of Baltic herring since the Viking Age revealed by ancient DNA and population genomics
inferred← citeshttps://doi.org/10.1101/782201openalex-snapshot
Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish
inferred← citeshttps://doi.org/10.1111/1755-0998.13551openalex-snapshot
An accurate assignment test for extremely low‐coverage whole‐genome sequence data
inferred← citeshttps://doi.org/10.1111/eva.12875openalex-snapshot
Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea
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