Reference transcriptomes for three species of sacoglossan sea slug
Caplins, Serena (2021), Reference transcriptomes for three species of sacoglossan sea slug, Dryad, Dataset, https://doi.org/10.25338/B8F33P
Understanding how species may respond to climate change is of paramount importance. Species that occupy highly heterogenous environments such as intertidal zone estuarine habitats, provide an ideal test case for examining phenotypic and genomic adaptations to different environmental conditions, which may influence their response to rapidly shifting climatic conditions. The California coast is projected to experience changes in both temperature and salinity, which currently vary seasonally and latitudinally. Using comparative transcriptomics, I documented patterns of positive selection between the northern dwelling planktotrophic sacoglossan sea slug Alderia modesta which is remarkably tolerant of low temperatures and low salinities and its southern congener Alderia willowi which exhibits a striking flexibility for larval type in response to seasonally shifting changes in temperature and salinity. Out of over four thousand one-to-one orthologous genes, I found a signal of positive selection between Alderia willowi and A. modesta for genes involved in cell membrane and cell transport, particularly ion homeostasis (Aquaporin), cell-cell signal transduction, and phosphorylation (NADH dehydrogenase) Positive selection for ion homeostasis in A. modesta has implications for its ability to tolerate the lower salinity of its northern range and in A. willowi substitutions in NADH may assist in high temperature tolerance of its southern California habitats. Identifying these candidate genes enables future studies of their functionalization as we seek to understand the relationship between phenotype and genotype in species whose phenotypes are influenced by environmental conditions.
de novo reference transcriptome assembly
Prior to de novo transcriptome assembly, adapters were removed and reads were quality trimmed in Trimmomatic using parameters for paired reads, removing leading a trailing low quality base pairs (LEADING:2 TRAILING:2), and a sliding window of 4 base-pairs removing basepairs when quality drops below 15 (SLIDINGWINDOW:4:15, and keeping reads of a minimum length of 25 (MINLEN:25)(Faircloth 2013 ). Trimmed reads were assembled in Trinity (v2.4.0) using default parameters (Haas et al., 2013). I assessed assembly quality with BUSCO (Simão et al., 2015) against the metazoan and eukaryote databases.
Three reference transcriptomes for the following sacoglossan species: Alderia modesta, Alderia willowi, and Olea hansineensis in fasta format.