Overview

The Southern Ocean salp, Salpa thompsoni (Tunicata, Thaliacea) is a pivotal species in the pelagic ecosystem of the Western Antarctic Peninsula (WAP), one of the fastest warming regions of the world oceans. This study produced the first reference genome and reference transcriptome for S. thompsoni. The genomic resources provide a significant step forward in the development of the salp as a model species for studying urochordate evolution; adaptation to a polar, planktonic environment; and the molecular processes underlying organism-environment interactions of this species. The transcriptomic resources will allow improved mechanistic understanding and prediction of impacts and consequences of environmental variation and climate change on the population dynamics and adaptation potential of this key species in the Southern Ocean pelagic ecosystem. Overall, the S. thompsoni reference genome and transcriptome provide important reference points for the continued understanding of the adaptive evolution of polar and planktonic species, as well as the elucidation of the underlying biology of an important group of chordate-related organisms. 

Intellectual Merit

We have also assembled the first draft genome sequence for S. thompsoni, as well as the first estimates of genome size and gene predictions for this species. This assembly, while still in need of further study and more data, was used to establish an extensive resource of gene, repetitive element, and small RNA gene predictions. The genomic data have established significant resources for both further phylogenomic and population genetic studies. Patterns in protein divergence in S. thompsoni appear to confirm the urochordate characteristic of elevated rates of genome evolution, indicating that urochordates may be particularly responsive to selective pressures. For instance, genome size, repetitive element content and patterns of positive selection in ribosomal genes indicate that expansion of rDNA gene families is extensive in this species, and and may be related to metabolic adaptations to polar environments. Additionally, the rapid evolution of the variably expressed gene cyclophilin A supports the functional importance of immune gene in urochordate biology, specifically the unusual complex life history, with both solitary and colonial stages. This rate of evolutionary change is also notable in the small RNA repertoire of this species that is characterized by both conserved and novel miRNAs implicated in embryonic development, as well as a possibly novel piRNA biogenesis mechanism.

The S. thompsoni reference transcriptome contains 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) were mapped and annotated. The new data will provide a foundation for functional analysis and identification of molecular markers of physiological condition and life history events. Whole-transcriptome (RNA-seq) analysis of 39 samples collected during austral spring and summer 2011 in the WAP, and in summer 2009 in the Indian Sector revealed clustering of samples by regions, seasons, and areas. Patterns of differential gene expression revealed notable differences between salp samples collected from different regions, seasons, and areas of the Southern Ocean. A primary result was the finding of highest numbers of significantly differentially expressed genes between spring and summer 2011 collections from the Western Antarctic Peninsula (WAP) region. This difference was also reflected by high levels of differential expression for 77 genes associated with environmental stress response and 51 genes associated with sexual reproduction. Gene Ontology (GO) term enrichment analysis of salps collected during spring versus summer in the WAP showed 41 GO terms responsible for the changes in gene expression pattern between the spring and summer seasons.

Broader Impacts

Outreach and education activities included three experiential workshops for high school teachers (2012, 2013, 2015), which provided foundations for new learning goals and new curriculum elements related to the molecular analysis of marine organisms. Hands-on exercises included DNA barcoding and DNA sequence analysis; lectures and discussions focused on impacts of climate change, global warming, ocean acidification, and disruption of biological communities. A fourth workshop (2016) for high school students (accompanied by their teachers) was held to directly evaluate resulting curriculum modules. Our assessment process indicated that our workshops may have impacted 200 – 400 students, who were exposed to novel classroom, laboratory, and computer exercises in science education.

Last Modified: 08/29/2016
Modified by: Ann C Bucklin