ArticleGenome biology2016
The genome of the Gulf pipefish enables understanding of evolutionary innovations.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 95 citations in OpenAlex.
- Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids.Integrative zoology · 2026Article
- Lineage-specific change in craniofacial gene regulatory networks of syngnathid fishes revealed by integrating multiomics across fishes.bioRxiv : the preprint server for biology · 2026Article
- Signatures and likely sources of the male pregnancy microbiome in wild bay pipefish (Syngnathus leptorhynchus).Animal microbiome · 2025Article
- Symbiosis with and mimicry of corals were facilitated by immune gene loss and body remodeling in the pygmy seahorse.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sexual Selection on Non-Ornamental Traits Is Underpinned by Evidence of Genetic Constraints on Sex-Biased Expression in Dusky Pipefish.Molecular ecology · 2025Article
- Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.Genome biology and evolution · 2025Article
- Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).The Journal of heredity · 2025Article
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- Are fish immunocompetent enough to face climate change?Biology letters · 2024Review
- WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino acids.Bioinformatics advances · 2024Article
- Near chromosome-level and highly repetitive genome assembly of the snake pipefishGigaByte (Hong Kong, China) · 2024Article
- A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation.Genomics, proteomics & bioinformatics · 2023Article
- The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation.Genomics, proteomics & bioinformatics · 2023Article
- The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling.Science China. Life sciences · 2023Article
- Article
- Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.Molecular biology and evolution · 2023Article
- Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species.Molecular biology and evolution · 2023Article
- Improvements to the Gulf pipefishGigaByte (Hong Kong, China) · 2023Article
- Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundEvolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch.
resultsWe produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions.
conclusionsThe collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups.
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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.