A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata 1

24 Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts 25 from the algae they consume. These ‘photosynthetic animals’ incorporate stolen chloroplasts, 26 called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts 27 throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts 28 in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the 29 saccoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys 30 that can retain photosynthetically active kleptoplasts for several months without feeding. We 31 used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to 32 produce a 786 Mbp assembly containing 68,514 predicted protein-coding genes. A phylogenetic 33 analysis found no evidence of horizontal acquisition of genes from algae. We performed gene 34 family and gene expression analyses to identify E. crispata genes unique to kleptoplast-35 containing slugs that were more highly expressed in fed versus unfed developmental life stages. 36 Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes 37 encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive 38 oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four 39 polyketide synthase genes that could potentially encode proteins producing UV-and oxidation-40 blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource 41 that provides potential targets for functional analyses and enables further investigation into the 42 evolution and mechanisms of kleptoplasty in animals.