ArticleGenome research2019
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 177 citations in OpenAlex.
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- Unheralded high MHC class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing.Science advances · 2026Article
- Multiple modes of selection underlie repeated and human-mediated adaptation in a formerly migratory fish.Molecular biology and evolution · 2026Article
- Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes.bioRxiv : the preprint server for biology · 2026Article
- Conserved differential expression of DDX helicase and CPEB genes in skeletal muscles potentially influences neuromuscular junctions during aging: a computational analysis.Biogerontology · 2026Article
- A chromosome-level reference genome for Pacific herring (GigaByte (Hong Kong, China) · 2026Article
- Population Genomics Provides Novel Insights Into Evolutionary Relationships and Local Adaptation of Two EcotypesEcology and evolution · 2025Article
- Genome-Wide Population Structure in a Marine Keystone Species, the European Flat Oyster (Ostrea edulis).Molecular ecology · 2025Article
- Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments.Molecular ecology · 2025Review
- Biogeographic Structure and Mitonuclear Discordance Reveal Cryptic Diversity in Pacific Herring (Ecology and evolution · 2025Article
- Reference genome bias in light of species-specific chromosomal reorganization and translocations.Genome biology · 2025Article
- Population Patterns and Dynamics ofEvolutionary applications · 2025Article
- Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.BMC genomics · 2025Review
- Evolution of fast-growing piscivorous herring in the young Baltic Sea.Nature communications · 2024Article
- A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity.npj biodiversity · 2024Review
- The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA.Global change biology · 2024Article
- Genetics in the Ocean's Twilight Zone: Population Structure of the Glacier Lanternfish Across Its Distribution Range.Evolutionary applications · 2024Article
- The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring.Nature communications · 2024Article
- Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish.Evolutionary applications · 2024Article
- Genomic architecture and population structure of Boreogadus saida from Canadian waters.Scientific reports · 2024Article
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Authors and funding
19 authors at 6 institutions in 7 countries.
Funding
Abstract
The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.