Methods
A subset of specimens was collected from the La Jolla Tide Pools in La Jolla, CA, USA in December 2022 (Aegires albopunctatus McFarland, 1905, Ancula gibbosa (Risso, 1818), and Dendronotus venustus McFarland, 1966). These specimens were collected by hand while tide pooling. Foot, tail, or whole animal tissues were taken from these and historical specimens in the Malacology collection at the American Museum of Natural History. Most of the included historical specimens were collected in the 1990s (Corambe burchi (Er. Marcus & Ev. Marcus, 1967), Doris verrucosa Linnaeus, 1758, and Scyllaea pelagica Linnaeus, 1758), with the exception of Aeolidia papillosa (Linnaeus, 1761), which was collected in 1910.
DNA extraction was performed with the Qiagen DNAeasy Genomic Extraction Kit using a standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit, according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in a paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions using Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled using SPAdes v2.5 (Bankevich et al. 2012) followed by a final assembly finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Results and Data Availability
All raw read data and assembled genomes are available in the GenBank database.
Funding
Funding was provided by the Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.