Project Information
Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa thompsoni
Short Title:
Genome Assembly of Salpa thompsoni
Start Date:
End Date:
The Antarctic salp, Salpa thompsoni, is an increasingly important player in the vulnerable Southern Ocean pelagic ecosystem. Field studies have documented rapid population growth under favorable environmental conditions, resulting in dense blooms of salps that can out-compete and displace other species, and significantly perturb the pelagic ecosystem. A comprehensive reference genome for the Antarctic salp will enable the identification of genes and gene networks underlying physiological responses and allow detection of natural selection driving the species’ adaptation to climate change. The primary hypothesis driving this research is that predicted S. thompsoni orthologs (i.e., genes of the same function that share a common ancestor) that show evidence of rapid evolution are indicative of positive selection, and further that these genes and associated gene networks provide the basis for rapid adaptation of the Antarctic salp to environmental variation associated with climate change. Our genome assembly strategy builds upon methods developed during our previous award (PLR-1044982), including both paired-end short read and linked-read sequencing approaches. 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.
Person Role
Bucklin, Ann Investigator and contact
O'Neill, Rachel J Co-Investigator
Antarctic Organisms and Ecosystems Award # 1643825
AMD - DIF Record(s)
Data Management Plan
None in the Database
Product Level:
0 (raw data)
  1. Bucklin, A. K. DiVito, I. Smolina, M. Choquet, J.M. Questel, G. Hoarau and R.J. O’Neill (2018) Population Genomics of Marine Zooplankton. In: Population Genomics. Springer, Cham (doi:
  2. O’Neill, M. J., & O’Neill, R. J. (2018). Sex chromosome repeats tip the balance towards speciation. Molecular Ecology, 27(19), 3783–3798. (doi:10.1111/mec.14577)
  3. O’Neill, R. J. (2020). Seq’ing identity and function in a repeat-derived noncoding RNA world. Chromosome Research, 28(1), 111–127. (doi:10.1007/s10577-020-09628-z)
  4. Brown, J., Crivello, J., & O’Neill, R. J. (2018). An updated genetic map of Peromyscus with chromosomal assignment of linkage groups. Mammalian Genome, 29(5-6), 344–352. (doi:10.1007/s00335-018-9754-7)
  5. O’Neill, R. J., & O’Neill, M. J. (2018). Replication timing kept in LINE. Journal of Cell Biology, 217(2), 441–443. (doi:10.1083/jcb.201712173)
Platforms and Instruments

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