Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus

Abstract

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.

Keywords: Hi-C Chicago; ONT; Pomacentridae; Robertsonian polymorphism; chromosome fusion; coral reef fish; domino damselfish; hybrid genome assembly; illumina shotgun.

Fig. 1.

Dascyllus trimaculatus and species complex global distribution. The three-spot damselfish (Pacific morph) is shown on the right of the map adapted from Leray et al. (2009) and Salas et al. (2020). The map shows in blue the broad distribution of D. trimaculatus. Differences in blue reflect results of Salas et al. (2020) which showed Indian Ocean differentiation from Pacific populations as well as a sub population in Cocos Keeling and a hybridization zone in Christmas Island. Similarly, the darker blue patch in the Central Pacific shows another divergent population of D. trimaculatus identified in Leray et al. (2009). The other colors show the distributions of the other species within the D. trimaculatus complex: green for D. albisella, yellow for D. auripinnis, and red for D. strasburgi.

Fig. 2.

Genome statistics and chromosome map. Panel A: The outer circumference of the main plot represents the full length of the 910,763,285 bp chromosome-scale assembly of Dascyllus trimaculatus. The outer ring of blues depicts GC (dark blue) and AT (light blue) content along the assembly which is summarized in the lower left. The second ring is demarcated by percentage of the total contigs of the genome. Orange and pale-orange arcs show the N50 and N90 record lengths (34,909,338 and 22,085,708 bp), respectively, overlying the dark gray, which arranges scaffolds in order by size starting from the largest scaffold (41,400,476 bp and ∼4% genome, shown in red). A summary of BUSCO statistics for complete (97.9%), fragmented (0.7%), duplicated (1.7%), and missing (1.5%), orthologous genes in the actinopterygii_odb10 set is shown in the top right. Panel B: A Hi-C contact map made with the MluCI and the DpnII libraries showing 24 chromosome clusters and the unscaffolded contigs. In the green square, chromosomes 3 and 4 show strong interchromosomal connections at roughly half coverage indicating Robertsonian fusion in one set of chromosomes contributed a parent with 2n = 47 while the other parent contributed 2n = 48.

Fig. 3.

Dascyllus trimaculatus mapped against chromosome-level genome of Amphiprion percula (Pomacentridae). The main panel shows a dot-plot of the assemblies of Dascyllus trimaculatus (presented in this manuscript) and the genome of the anemone fish Amphiprion percula (Lehmann et al. 2019). The remaining unscaffolded contigs are shown in the last column. The right three panels show a close-up dot-plot of the color-coded boxes in the main panel of chromosome 3, chromosome 7, and chromosome 24. Chromosome 3, one of the chromosomes involved in Robertsonian fusions within the species, shows many rearrangements as well as regions of repeat sequences near one end. Chromosome 7 seems to be one of the most architecturally conserved chromosomes between Dascyllus and Amphiprion, whereas Chromosome 24 shows an example of a highly rearranged chromosome.