Date of Completion

Spring 5-3-2024

Thesis Advisor(s)

J Wegrzyn; C Garcia-Robledo

Honors Major

Biological Sciences

Disciplines

Bioinformatics | Biology | Ecology and Evolutionary Biology | Genetics and Genomics

Abstract

Cold-water corals are important sources of ocean biodiversity, yet populations are increasingly threatened by human activity and climate change. Soft octocorals may endure higher ocean acidification levels in comparison to stony hexacorals, although the mechanisms of octocoral biomineralization are less understood. Building genomic resources for cold-water octocorals could help to close information gaps by elucidating the evolutionary history of octocoral calcification and provide a reference for future studies of adaptation to acidified waters. This report describes the first reference genome for the cold-water octocoral species Anthothela grandiflora found throughout the Atlantic Ocean. Sequencing using Oxford Nanopore Technologies generated 43.6 Gb of long reads at 35.9x coverage. The final reference genome was 641 Mb in length, contained 22,669 scaffolds with an N50 length of 82.5 Kb, and included 84.1% of the expected metazoan single-copy orthologs. A high proportion of repetitive content (67.8%) was masked from the genome. Illumina sequencing generated 32.9 Mb of paired-end RNASeq reads for genome annotation to identify 14,837 protein-coding genes with a BUSCO completeness of 81.80%. Orthologous gene family analysis was used to identify 5 expanded and 155 contracted gene families specific to A. grandiflora, many of which relate to metabolic and biosynthetic processes, immune and stress response, and ion binding. These genomic resources will augment the current understanding of soft corals and benefit the protection of ecologically-important cold-water coral communities.

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