Salps in Bloom: Genome Dynamics Provide Insight into the Reproductive Success of Salpa thompsoni and Salpa aspera

• Other Authors: Castellano, Kate (Creator), O'Neill, Rachel J. (Major Advisor), Bucklin, Ann (Associate Advisor), Wegrzyn, Jill (Associate Advisor), O'Neill, Michael (Associate Advisor), Mellone, Barbara (Associate Advisor), University of Connecticut (Degree grantor)
• Format: Text
• Language: unknown
• Published: University of Connecticut 2021
• Subjects: Southern Ocean; North West Atlantic
• Online Access: http://hdl.handle.net/11134/20002:860664848; https://digitalcollections.ctstatelibrary.org/islandora/object/20002%3A860664848/datastream/TN/view/Salps%20in%20Bloom%3A%20Genome%20Dynamics%20Provide%20Insight%20into%20the%20Reproductive%20Success%20of%20Salpa%20thompsoni%20and%20Salpa%20aspera.jpg

Warming trends in Ocean “hot spot” regions have altered trophic dynamics in favor of pelagic tunicates which are showing rapid population expansion (blooms) that displace other key species. Two of these regions are the Southern Ocean and the North West Atlantic, dominated by Salpa thompsoni and Salpa aspera respectively. Salp blooms are facilitated by their reproductive life history, which consists of seasonal alternations between asexual and protogynous (or sequential) hermaphroditic sexual stages. However, we lack a foundational understanding of the genomic features that define these species and support bloom formation. Genomic resources are overall lacking for many tunicates with only 18 out of >2,000 known species having assembled genomes. S. thompsoni is the only pelagic tunicate with an available reference assembly which is both incomplete and fragmented making inferences about their biology difficult. Short-read sequencing approaches have failed to generate a quality genome assembly for salp, likely the result of the high repeat content previously identified in the draft S. thompsoni genome. Herein, using Oxford Nanopore long-read sequencing and de novo assembly, I have derived an improved assembly for S thompsoni and an additional assembly for a congeneric species, S. aspera. Both genomes uncovered an 80% repeat abundance, 20% higher than predicted and the highest of all reported tunicate species. Further genome analysis revealed an abundance of G-quadruplex (G4) motifs distributed around genes and repeats. In addition to genomic references, a transcriptome from 21 samples encompassing sexual and asexual adult and embryonic stages was developed for S. thompsoni to better understand genes and pathways required for alternating reproductive life histories. Differential expression analysis identified male sex differentiation and spermatogenesis genes as early as stage 2 in conjunction with female reproductive genes suggesting salp are hermaphroditic, challenging the traditional view of protogynous ...