Fig. 2

Experimental flow for screening tissue-specific effector genes. Screening of tissue-specific effector genes was conducted from the gene models of H. pulcherrimus genome in multiple steps. (1) Transcription factors and signaling molecules were removed based on the domain structure. (2) The genes that did not show reciprocal BLAST best hits between H. pulcherrimus (Hp) and S. purpuratus (Sp) were excluded. (3) Genes whose expression was biased to specific cell lineage(s) in single-cell RNA-seq data from S. purpuratus were selected. The average of expression levels (Ave. exp.) was calculated in each cell cluster (0–14) and gene. We counted the number of cell lineages in which the expression level was higher than 0.3 for each gene (#: the number of cell lineages). Three examples were shown in 0, 1 and 7 lineage(s). (4) Zygotic expression onset of the genes was determined using temporal transcriptomic data from H. pulcherrimus. (5) Gene annotations were checked manually to refine the sets of tissue-specific effector genes. See the text for detailed methods and results