Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores

Abstract

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.

Keywords: k-mer spectra; genome size; genome skimming; mitochondrial genomes.

Fig. 1.

Photographs of some siphonophore species included in this study by CWD and SHD. Lengths are approximate. a) Physalia (float is about 20 mm across). b) Frillagalma vityazi (about 8 cm long). c) Nanomia bijuga (about 5 cm long). d) Apolemia rubriversa (specimen image about 7 cm across). e) Gymnopraia lapislazula (nectophore is about 2 cm across).

Fig. 2.

Number of nuclear genomes sequenced across Cnidaria, including both scaffold and chromosome-level assemblies. Siphonophores are within Hydroidolina, a subclade within Hydrozoa.

Fig. 3.

Plots of k-mer spectra for samples with peaks. Model fit is assessed by whether the full model curve (outer curved line) has peaks congruent with the underlying k-mer spectrum. The reported genome sizes for the specimens with poor model fit, indicated by asterisks, are from the Jellyfish counting.

Fig. 4.

GenomeScope convergence for eight siphonophore species shown in Fig. 3. Vertical lines indicate where the models reached 95% model fit, in the six specimens with good model fit.

Fig. 5.

Diversity of siphonophore mitochondrial gene order. Squares indicate nodes constrained to be congruent with Munro et al. (2018). None of the constrained nodes had strong conflict between the mitochondrial and nuclear data; they were well supported in the nuclear data and had poor support in the mitochondrial data (see supplementary fig. S6, Supplementary Material online, for the unconstrained mitochondrial phylogeny). Bootstrap values less than 100 are indicated at the nodes; where no numerical value is indicated at unconstrained nodes, the bootstrap value is equal to 100. Mitochondrial rRNA and protein-coding gene arrangements of siphonophores are depicted on the right. cox1_c is an incomplete copy of cox1 and lacks the 5′ end of the gene.

Fig. 6.

Cnidarian genome sizes and genome size estimates arranged by group. All Siphonophora represented here are newly sequenced for this project and are bolded.