Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

Abstract

Background: Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.

Results: In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.

Conclusions: We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

Keywords: Elysia timida; Arima HiC; Biosynthesis; High-quality reference genome; Kleptoplasty; Mollusca; PacBio HiFi; Polyketides; Sacoglossa.

Fig. 1

The Sacoglossa Elysia timida [24] (a) and its unicellular food algae Acetabularia acetabulum (b). Photos were taken by C. Greve

Fig. 2

Contact map after yahs scaffolding using Arima HiC data and manual curation. Blue and green squares mark scaffolds and contigs, respectively. Higher number of contacts is represented by higher intensity of the colour

Fig. 3

Snail plot of the final genome assembly. The plot created with blobtoolkit visualizes amongst others scaffold count, lengths, length distribution, nucleotide composition, and recovered BUSCOs

Fig. 4

Excerpt of a molecular network showing detected polypropionates from crude extracts of E. timida. Putative polypropionates were clustered based on their similar MS/MS fragmentation patterns. Each node represents a polypropionate and is labelled with the detected mass. Masses that correspond to characterized polypropionates are color-coded. White nodes correspond to putative polypropionates that were not characterized yet. The node size corresponds to the production level and the edge width represents the relatedness between two compounds. The thresholds for the cluster were set to 7 minimum matched peaks and a cosine score of 0.6