Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa thompsoni

This project used state-of-the-art approaches: Oxford Nanopore long read sequencing, de novo assembly, and comprehensive transcriptomics. The results include a new reference genome for S. thompsoni, consisting of 8,815 sequences (contigs), with less fragmentation (N50 = 188 kb), and genome coverage of 78%. We have discovered strong secondary structures that dramatically affect sequencing efficiency.

Our analyses of these secondary structures led to the discovery of abundant G-quadruplex sequences distributed throughout the genome at a significantly higher frequency compared to other tunicate species, suggesting the structures are a defining feature of this salp genome. These results provide novel insights into the function of unique genomic features in the regulation of genome stability, despite the complex life history, including sexual and asexual reproduction of the Southern Ocean salp.

The completed salp reference genome will provide a valuable foundational resource for other scientists (including ecologists, oceanographers, and climate change experts), working on this species.