loading page

Chromosome-scale genome assemblies for 10 syngnathiform fishes produced using a standardized sequencing and annotation workflow
  • +11
  • Balan Ramesh,
  • Clay Small,
  • Susan Bassham,
  • Bernadette Johnson,
  • Elyse Barker,
  • Emily Rose,
  • Mark Currey,
  • Hope Healey,
  • Megean Myers,
  • Ingrid Ahnesjö,
  • Lotta Kvarnemo,
  • Nuno Monteiro,
  • William Cresko,
  • Adam Jones
Balan Ramesh
University of Idaho

Corresponding Author:[email protected]

Author Profile
Clay Small
University of Oregon Institute of Ecology and Evolution
Author Profile
Susan Bassham
University of Oregon Institute of Ecology and Evolution
Author Profile
Bernadette Johnson
University of Idaho College of Science
Author Profile
Elyse Barker
University of Idaho College of Science
Author Profile
Emily Rose
Valdosta State University
Author Profile
Mark Currey
University of Oregon Institute of Ecology and Evolution
Author Profile
Hope Healey
University of Oregon Institute of Ecology and Evolution
Author Profile
Megean Myers
University of Idaho College of Science
Author Profile
Ingrid Ahnesjö
Uppsala University Division of Animal Ecology
Author Profile
Lotta Kvarnemo
University of Gothenburg
Author Profile
Nuno Monteiro
CIBIO, Campus de Vairão
Author Profile
William Cresko
University of Oregon Institute of Ecology and Evolution
Author Profile
Adam Jones
University of Idaho
Author Profile

Abstract

Over the past 65 million years, fishes in the family Syngnathidae (seahorses, pipefishes, and seadragons) have diversified into over 300 species that are globally distributed in marine and brackish environments, as well as in a small number of freshwater habitats. This clade is noteworthy for unusual species possessing novel and highly derived phenotypes, such as male pregnancy, elongated faces, prehensile tails, and ornate dermal outgrowths. Many of these traits evolved convergently in multiple lineages against the backdrop of the characteristic pipefish elongated phenotype. Though this family offers a rich system to explore developmental evolution in a vertebrate lineage, analysis of the genetic underpinnings of these traits has been hampered by a lack of high-quality, annotated genome assemblies for most syngnathid species. Here, we begin filling this gap by presenting high-quality, chromosome-scale genome assemblies for ten species from the Order Syngnathiformes. These assemblies, which we produced using a common assembly and annotation workflow, encompass nine syngnathid fishes and one outgroup species. We assembled each genome using PacBio High Fidelity reads and Hi-C contact maps and annotated them using the NCBI Eukaryotic Genome Annotation Pipeline. All nine genome assemblies are highly contiguous (with N50 values between 14Mb and 75Mb) and nearly complete (with BUSCO scores ranging from 97.6% to 99.6%). Assembled genomes range in size from 428 million base pairs to 3.1 billion base pairs, a pattern that likely resulted from lineage-specific genome duplication and repetitive DNA expansion and contraction. These ten genome assemblies are available publicly as RefSeq genome resources, providing a significant foundation for comparative genomic and functional genetic research on the wealth of fascinating syngnathid phenotypes.