ArticleGenome biology and evolution2019
A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 87 citations in OpenAlex.
- Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis.Genes & genomics · 2026Article
- A near telomere-to-telomere genome assembly of the Amur stickleback (Zoological research · 2026Article
- Nest architecture and male aggression drive sexual isolation between three-spined stickleback ecotypes.Zoological letters · 2026Article
- A Y-linked duplication of anti-Mullerian hormone is the sex determination gene in threespine stickleback.PLoS genetics · 2025Article
- Single cell RNA-sequencing reveals no evidence for meiotic sex chromosome inactivation in the threespine stickleback fish.PLoS genetics · 2025Article
- Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.Genome biology and evolution · 2025Article
- Single cell RNA-sequencing reveals no evidence for meiotic sex chromosome inactivation in the threespine stickleback fish.bioRxiv : the preprint server for biology · 2025Article
- Estimating Recent and Historical Effective Population Size of Marine and Freshwater Sticklebacks.Molecular ecology · 2025Article
- Rate of de novo mutations in the three-spined stickleback.Heredity · 2025Article
- Dynamics of Deleterious Mutations and Purifying Selection in Small Population Isolates.Molecular biology and evolution · 2025Article
- Discrete genetic modules underlie divergent reproductive strategies in three-spined stickleback.bioRxiv : the preprint server for biology · 2025Article
- Same trait, different genes: pelvic spine loss in three brook stickleback populations in Alberta, Canada.Evolution letters · 2025Article
- Improved assembly of the Pungitius pungitius reference genome.G3 (Bethesda, Md.) · 2024Article
- Host ecotype and rearing environment are the main drivers of threespine stickleback gut microbiota diversity in a naturalistic experiment.Royal Society open science · 2024Article
- Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure.BMC genomics · 2024Article
- Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks.Molecular biology and evolution · 2024Article
- Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2024Article
- Differential gene expression and developmental pathologies associated with persistent organic pollutants in sentinel fish in Troutman Lake, Sivuqaq, Alaska.Environmental pollution (Barking, Essex : 1987) · 2024Article
- Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map.Heredity · 2023Article
- Fast satellite DNA evolution in Nothobranchius annual killifishes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
Indexed as
Identifiers
What OpenQuestion holds
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.