Chromosome-scale genome assemblies for 10 syngnathiform fishes produced
using a standardized sequencing and annotation workflow
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.