ArticleThe Journal of heredity2017
Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.
Article in The Journal of heredity, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
41 citing papers in PubMed, 78 citations in OpenAlex.
- Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.Genome biology and evolution · 2026Article
- Variable jackpot individuals provide most alleles for repeated, rapid adaptation to freshwater by anadromous Threespine Stickleback.bioRxiv : the preprint server for biology · 2026Article
- Rare jackpot individuals drive rapid adaptation in Threespine Stickleback.Nature communications · 2026Article
- Changes in gene regulation are associated with the evolution of resistance to a novel parasite.Frontiers in immunology · 2026Article
- Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet.G3 (Bethesda, Md.) · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.The plant genome · 2025Article
- Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement.Plant biotechnology journal · 2024Article
- A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus.Scientific data · 2023Article
- Single-Cell RNA Sequencing Reveals Microevolution of the Stickleback Immune System.Genome biology and evolution · 2023Article
- Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks.Molecular biology and evolution · 2023Article
- Predicting recombination frequency from map distance.Heredity · 2023Article
- Evaluating Dermal Bone as a Novel Source of Endocrine Information in Ninespine and Threespine Stickleback Fish.Integrative organismal biology (Oxford, England) · 2023Article
- Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits.G3 (Bethesda, Md.) · 2022Article
- Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback.Genome biology and evolution · 2022Article
- Comparing genome scans among species of the stickleback order reveals three different patterns of genetic diversity.Ecology and evolution · 2022Article
- Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions.Frontiers in genetics · 2022Article
- Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.Molecular ecology resources · 2021Article
- Threespine Stickleback: A Model System For Evolutionary Genomics.Annual review of genomics and human genetics · 2021Review
- The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions.Parasites & vectors · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage groups (LGs), with ordering nearly identical to the previous genome assembly. Using available bacterial artificial chromosome (BAC) end sequences, we provide evidence that some of the few discrepancies between the Hi-C assembly and the existing assembly are due to structural variation between the populations used for the 2 assemblies or errors in the existing assembly. This Hi-C assembly also allowed us to improve the existing assembly, assigning over 60% (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to LGs. Together, our results highlight the potential of the Hi-C based PGA method to be used in combination with short read data to perform relatively inexpensive de novo genome assemblies. This approach will be particularly useful in organisms in which it is difficult to perform linkage mapping or to obtain high molecular weight DNA required for other scaffolding methods.
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Registered trials
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.