title: The genome of the Gulf pipefish enables understanding of evolutionary innovations.
abstract: Evolutionary 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.
  
  
  
  We 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.
  
  
  
  The 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.
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
authors.forename: C M
authors.initials: CM
authors.lastname: Small
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
authors.forename: S
authors.initials: S
authors.lastname: Bassham
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.|Present address: Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: J
authors.initials: J
authors.lastname: Catchen
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA.
authors.forename: A
authors.initials: A
authors.lastname: Amores
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
authors.forename: A M
authors.initials: AM
authors.lastname: Fuiten
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.|Present address: Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: R S
authors.initials: RS
authors.lastname: Brown
authors.affiliation: Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
authors.forename: A G
authors.initials: AG
authors.lastname: Jones
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA. wcresko@uoregon.edu.
authors.forename: W A
authors.initials: WA
authors.lastname: Cresko
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002875:Chromosomes / Q000235:genetics; D005260:Female; D016678:Genome; D008297:Male; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010802:Phylogeny; D011247:Pregnancy; D012098:Reproduction / Q000235:genetics* / Q000502:physiology; D017422:Sequence Analysis, DNA; D012727:Sex Characteristics; D023701:Smegmamorpha / Q000235:genetics* / Q000502:physiology
keywords: Differential expression; Evolution; Gene loss; Genome assembly; Male pregnancy; Novel traits; Syngnathidae; Syngnathus scovelli