Chromosomal-level genome assembly of the bioluminescent cardinalfishSiphamia tubifer, an emerging model for symbiosis research

Abstract

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly of S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of the S. tubifer genome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique to S. tubifer in which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ of S. tubifer. We also assembled the complete mitogenome of S. tubifer and discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestral Siphamia species. This draft genome assembly of S. tubifer will enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.