Sequence similarity, ortholog analysis, and gene content comparison

Pairwise sequence comparisons between L. chagosensis and other sponge species were performed using Blastp alignments at an e-value cutoff of 1 x 10−5. Orthologous gene families in the transcriptome of L. chagosensis and in the genomes or transcriptomes of other sponge species were identified using OrthoFinder (Emms and Kelly 2019). Predicted peptide sequences of representative sponge species were annotated against the Pfam 32.0 (Finn, et al. 2014) database and were assigned to their associated GO terms based on Blastp top hits (e-value ≤1 x 10−5) in UniProtKB/Swiss- Prot database. Percent abundance was computed relative to the total number of predicted peptides in each species. Protein families and molecular functions that distinguish calcareans from other sponges (LDA score ≥ 2, p < 0.05) were determined using Linear Discriminant Analysis effect size (LDALEfSe) (Segata, et al. 2011).