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.

Variation among host-associated microbiomes is well documented across species, populations, and individuals. Understanding relationships between host-genetic and microbial variation is important for predicting coevolutionary dynamics between hosts and their microbiota and is also biomedically relevant to understanding why some humans are more susceptible to chronic disorders like Inflammatory Bowel Diseases (IBD). Unfortunately, the relative contributions of host genetics and the environment to microbiome variation have been difficult to study. Human research shows that genetic variation influences microbiome differences but confounding environmental effects cannot be controlled experimentally. Isogenic laboratory models can be used in controlled environments but often focus on large-effect mutations and do not recapitulate genetic variation observed in nature. Thus, although important factors impacting the microbiome have been identified, few studies have tested for the direct influence of natural host-genetic variation on microbiome differences within a controlled environment. To address this, we performed a common garden experiment using laboratory lines of genetically divergent populations of threespine stickleback fish - an outbred model organism commonly used for determining the genetic basis of complex traits in the context of natural genetic variation. Using germ-free derivation of divergent lines and hybrids between them in this experimental framework, we detected a clear, positive association between stickleback genetic dissimilarity and microbiome dissimilarity. With RAD-seq data we identified regions of the genome that contributed most significantly to this relationship. Importantly, we also highlight that heritable morphological traits like body size -when correlated with microbiome composition - need consideration in future host-associated microbiome studies.