Results
On average, ~10 million raw Illumina Hiseq reads were obtained per sample. After quality trimming and removal of rRNA and algal endosymbiont components, an average of ~5.5 million paired reads were retained per sample. The transcriptome of purebred A. loripes contained ~291 k transcripts, and ~59 k transcripts were left after only retaining the longest isoforms and removal of small transcripts < 400 bp. See Table S2 for details of other transcriptomes used for preliminary analysis and evaluating treatment effect. A total of ~35 k transcripts found match in the NCBI nr databased and were of coral origin. Following the removal of duplicates and transcripts that consistently had zero or very low counts, 8800 transcripts were remained and used for downstream analyses.
Transcriptome-wide gene expression of the hybrids was similar to that of their maternal purebreds, yet distinct from their paternal purebreds and the reciprocal hybrids (Figures 1-4). Principal component analyses (PCA) showed similar expression patterns of the hybrid LT with its maternal purebred LL under both ambient and elevated conditions (Figure 1). The only exception was one LL purebred sample which showed separation with the others in principle component two (Figure 1). Gene expression of the reciprocal hybrid TL also clustered with its maternal purebred TT (but note that n = 1 for TT), and was separated with hybrid LT and its paternal purebred LL under both treatment conditions (Figure 1). Within an offspring group, gene expression did not differ between ambient and elevated conditions (Figure 1). At a log-fold change cutoff of 0.2, only 40 differentially expressed genes (DEGs) were identified between maternal purebred LL and its hybrid LT (Figure 2). In contrast, almost 2000 DEGs were identified between paternal purebred LL and its hybrid TL, as well as between the reciprocal hybrids LT and TL (Figure 2). Among these ~2000 DEGs, the hybrid LT and its maternal purebred LL shared 1343 genes that were differentially expressed from hybrid TL (Figure 2). Mitochondrial genes (~30) were included in the analysis, but none were found differentially expressed.
Maternal effects on gene expression were also evident in the heatmap of the 500 most variable genes across samples (Figure 3). The only exception was one purebred LL which clustered away from the other LL samples, and this was the same sample the showed separation in the PCA plot (Figure 1, 3). Among the DEGs with the highest log-fold change (i.e., four DEGs for paternal purebred LL compared to its hybrid TL, and seven DEGs for hybrid LT compared to hybrid TL with LFC > 5), three were shared genes between the two pairs of comparison (Figure 4). Unfortunately, most of these DEGs were annotated as uncharacterized proteins and hence their potential functions were unknown (Table S3). For gene ontology (GO) analyses, GO category “cytosol” (GO: 0005829) was underrepresented in both the comparisons between paternal purebred LL with its hybrid TL and between the reciprocal hybrids LT and TL, with 90 and 96 DEGs respectively in this category (Table S4). Note that “cytosol” is a very broad GO category and was comprised of 620 genes in this dataset. In addition, the GO category “membrane” (GO: 0016020) was also underrepresented in the comparison between paternal purebred LL and its hybrid TL (Table S4). This was also a broad GO category with 255 genes in this dataset and 27 of which were DEGs.