Early Invasion Genomic Resources for Xenia umbellata (Native to the Red Sea) and its Associated Dinoflagellate Symbionts in Puerto Rico

Abstract

The frequency of xeniid soft coral invasions on Caribbean coral reefs is increasing, with three alien species reported so far. Xenia umbellata (Anthozoa, Octocorallia, Malacalcyonacea, Xeniidae), native to the Red Sea, was first reported on Puerto Rico coral reefs in October 2023. Here, we present the first draft genome assembly and early-invasion genomic resources for the rapidly spreading X. umbellata and its dinoflagellate symbiont (Family Symbiodiniaceae) produced from a specimen collected five months after the initial report. Using deep Illumina metagenomic sequencing ([~]243X coverage), we obtained [~]272.4 million high-quality 150 bp reads. The X. umbellata draft genome assembly is 151.14 Mbp in length, composed of 27,739 scaffolds, with an N50 of 6,477,837 bp. GenomeScope2 predicted a haploid genome size of 171.6-171.9 Mbp and calculated a heterozygosity of 1.27-1.29%. This suggests that the assembly captures [~]88% of the X. umbellata genome, and the relatively high heterozygosity may indicate introduction from a genetically diverse wild population. Completeness was further supported by BUSCO analysis (anthozoa_odb12 lineage), which identified 91.4% complete and 3.9% fragmented BUSCOs. Furthermore, 555,596 sequences were identified as belonging to Symbiodiniaceae, of which 99.97% (n= 555,520) aligned to a Durusdinium reference genome, suggesting that the co-invading symbiont belongs to the genus Durusdinium. Establishing these genomic and symbiotic resources at an early stage of invasion provides a critical foundation for monitoring range expansion, investigating host-symbiont evolutionary dynamics, and identifying genomic features that may underlie the invasive potential of X. umbellata as it spreads across Puerto Rico and the wider Caribbean.