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Genome content flat files for comparative genomic analysis of seadragons and relatives

Citation

Small, Clayton (2022), Genome content flat files for comparative genomic analysis of seadragons and relatives, Dryad, Dataset, https://doi.org/10.5061/dryad.31zcrjdmf

Abstract

Seadragons are widely recognized for their derived and novel traits. Research and conservation efforts involving these unique fish species and their relatives have been hindered by a lack of genomic resources. From this project we present full, annotated genomes of leafy and weedy seadragons, which help uncover surprising features of gene family and genome architecture evolution that likely relate to extreme phenotypic traits in seadragons, pipefishes, and seahorses. These genomes are important research resources for the Syngnathidae, a diverse, morphologically exceptional group of vertebrates, and for comparative genomic study of vertebrates in general.

Methods

  • Genome annotations (genes and repetitive DNA) for seadragons and other teleost fishes using standard tools (e.g. Braker, RepeatModeler, RepeatMasker)
  • Custom compartive genomic analysis and visualization using R scripts, and associated data files
  • 10x draft genome assembly for Doryrhamphus excisus
  • de novo transcriptome assemblies for Syngnathus scovelli

Usage Notes

The contents of this data set are organized into three high-level directories:

  • analysis_code/ (contains R scripts and data files to perform downstream analyses described in the manuscript)
  • summary_files/ (contains braker gene annotations for 5 syngnathiform genomes and repeat annotations for 16 teleost genomes)
  • supplementary_assemblies/ (contains a draft 10x genome assembly for bluestripe pipefish - BP1_comb_355M_pseudohap.2.fasta.gz, and two de novo Trinity transcriptome assemblies for Gulf pipefish)

Funding

National Science Foundation, Award: 2015419