Author: Kate R Castellano,  PhD Candidate (University of Connecticut)

Designation: 

Description:
Warming trends in the Southern Ocean have altered trophic dynamics in favor of the pelagic tunicate, <em>Salpa thompsoni</em>, which is showing rapid population expansion (blooms), that displace other key species. Salp blooms are facilitated by their reproductive life history, which consists of seasonal alternations between sexual and asexual stages. However, we lack a foundational understanding of the genomic features that define this species and support salp bloom formation. Both paired-end short read and linked-read sequencing approaches have failed to generate a quality genome assembly for any salp species, likely the result of the high repeat content of the salp genome. Herein, using Oxford Nanopore long read sequencing, <em>de novo</em> assembly and comprehensive transcriptomics, we have derived a new assembly for <em>S. thompsoni</em>, consisting of 8,815 contigs, an N50 of 188 kb, and genome coverage of 78%. Through this work, we have discovered strong secondary structures within the <em>S. thompsoni</em> genome that dramatically affect sequencing efficiency. Our analyses of these secondary structures led to the discovery of abundant G-quadruplex sequences distributed throughout the <em>S. thompsoni</em> genome at a significantly higher frequency compared to other tunicate species, suggesting such structures are a defining feature of this salp genome. The link between these G-quadruplex sequences, <em>de novo</em> gene and repeat annotations and transcriptional profiles across life stages will be discussed. Collectively, out results provide novel insights into the function of unique genomic features in the regulation of genome stability between asexual to sexual reproduction.­­

Category: Scientific Program Abstract > Special Sessions > SS33 Ecological genomics