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Chromosome-Level Genome Assembly of the Bioluminescent Cardinalfish Siphamia tubifer: An Emerging Model for Symbiosis Research.
Gould AL
,
Henderson JB
,
Lam AW
.
Abstract
The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer-P. mandapamensis association to be used as a model for symbiosis research.
Fig. 1. (a) Hi–C contact heatmap for Siphamia tubifer. Black lines indicate chromosome boundaries. (b) Gene density distribution across the 23 chromosomes of the S. tubifer genome. (c) Circos plots depicting synteny between the genomes of S. tubifer and the orbiculate cardinalfish, Sphaeramia orbicularis (1.3 Gb) and (d) the mudskipper Periophthalmus magnuspinnatus (702 Mb). Each chromosome in the S. tubifer genome is represented by a distinct color, whereas the Sp. orbicularis and P. magnuspinnatus chromosomes are shown in dark and light gray, respectively. Links between the genomes represent single copy orthologs from the BUSCO Actinopterygii gene set.
Fig. 2. (a) Gene map of the complete mitogenome of Siphamia tubifer. All genes are labeled including the tRNA WANCY region as well as the control region and the approximate location of the goose hairpin (gh) within the control region. (b) Histogram depicting heteroplasmy in the length of the control region observed for the HiFi sequence reads spanning the entire region. (c) Maximum likelihood tree depicting the phylogenetic relationships of several cardinalfish species for which there is whole mitochondrial genome data available, including S. tubifer from this study, in relation to another member of the Apogonoidei clade, Kurtus gulliveri, and several species of gobies in the sister clade Gobioidei. Two Syngnathiformes species are included as an outgroup. The relationships are based on whole mitochondrial DNA sequences excluding the control region using the GTR + F+I + G4 model of substitution. Bootstrap support values (500 replicates) are listed at the nodes. The scale bar indicates nucleotide substitutions per site. Associated GenBank accession numbers for each species are listed in table S3, Supplementary Material online.
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