A. tenuis larvae express different genes during initial contact with three Symbiodinium strains.
Successful infection with each symbiont culture (Smic, Snat, and Stri) was confirmed by fluorescence microscopy in all treatment groups at 24 hpi (Supplementary Figure 1), and levels of planula larvae with symbiont cells at 24 hpi were about 30% for Smic, 6% for Snat, and 3% for Stri (Supplementary Table S1). We performed 3’ mRNA sequencing of Acropora tenuis larvae inoculated with Smic, Snat, and Stri and with no Symbiodinium exposure (apo-symbiotic) (Supplementary Table S2). At 1, 3, 6, 12, and 24 hpi, gene expression of all A. tenuis genes was compared between Symbiodinium-infected and uninfected groups. An average of five million RNA-Seq reads per sample were retained after quality trimming, 65% of which were mapped to A. tenuis gene models (n = 22,905, Supplementary Table S2). Non-metric multidimensional scaling (NMDS) based on gene expression levels showed clear differences in time post-inoculation, but not in treatment groups (Smic-, Snat-, and Stri-inoculated samples and control (apo-symbiotic) samples), indicating that overall, gene expression of A. tenuis larvae was not significantly affected by symbiont infection and species (Figure 1). When we compared gene expression levels between Smic-inoculated and control samples, the number of differentially expressed genes (DEGs) gradually increased with inoculation time (three genes at 3 hpi, five at 6 hpi, 106 at 12 hpi, and 392 at 24 hpi; Table 1). In contrast, larvae inoculated with Snat and Stri showed completely different transcriptomic responses (Table 1): 19 genes were differentially expressed in the Snat-inoculated samples and 49 genes in Stri-inoculated samples at 1 hpi (Supplementary Table S3). No gene expression changes were observed at 3 or 12 hpi in the presence of either Snat and Stri, and only one DEG was detected at 6 hpi in Snat- and Stri-inoculated larvae (Supplementary Table S3). Eight DEGs were detected at 24 hpi in Stri-inoculated larvae, but none in Snat-inoculated larvae (Supplementary Table S3).
Comparison of DEG repertoires between initial contact and symbiosis establishment.
In Smic-inoculated larvae, a limited number of DEGs was shared between time points (3 to 24 hpi) (Figure 2A), suggesting that gene expression changes of host corals were drastic during initial contact with native symbionts. Next, we compared the DEG repertoires at 24 hpi with a previous study analyzing transcriptomic responses of A. tenuis larvae during symbiosis establishment (4, 8, and 12 days post-inoculation (dpi)) 30. Six DEGs were observed at all time points, 24 hpi, and 4, 8, and 12 dpi (Supplementary Figure 2), and only 2 upregulated DEGs and 38 downregulated DEGs identified at 24 hpi in this study were also observed at 4 dpi (Supplementary Figure 2), indicating that DEG repertoires between initial contact and symbiosis establishment are independent, but that the limited array of genes that is constantly differentially expressed in both stages could be important for transition of symbiosis phases.
A. tenuis genes that respond to native symbionts during initial contact.
We annotated DEGs using BLAST homology searches against the Swiss-Prot database (Supplementary Table S3). Two, five, 80, and 42 genes were upregulated at 3, 6, 12, and 24 hpi, respectively (Figure 2B). Among those, 0% (0/2 genes), 20% (1/5), 28% (22/80), and 88% (37/42) of DEGs were annotated (Supplementary Table S3). One, 26, and 350 genes were downregulated at 3, 12, and 24 hpi, respectively (Figure 2B). Of those, 100% (1/1 gene), 69% (18/26), and 70% (246/350) of DEGs were annotated (Supplementary Table S3), indicating that upregulated DEGs involved in establishing symbiosis have no homologs that have been annotated yet.
DEGs with Swiss-Prot annotation were used to infer biological processes that occur in Smi-inoculated larvae. To ensure reliability, we focused on categories of UniProt keywords in which more than two annotated genes were detected at each time point. Upregulated DEGs belonging to seven and five categories and downregulated DEGs belonging to one and 28 categories were detected at 12 and 24 hpi, respectively (Table 2). Some categories, such as transport and biological rhythms, were commonly observed among both up- and downregulated DEGs at 24 hpi (Table 2). In A. tenuis, seven genes similar to core circadian genes were differentially expressed from 4 to 12 days post-Symbiodinium inoculation in the previous study 30, and three (CRY1: aten_s0034.g64 and ate_s0034.g66; TIMELESS: aten_s0021.g100) of them were also differentially expressed in Smic-inoculated larvae at 12 and 24 hpi, and Stri-inoculated samples at 1 hpi (Supplementary Figure S3), indicating that gene expression of core circadian rhythm-regulated genes changed as soon as they were inoculated with Symbiodinium. When A. tenuis larvae were inoculated with native symbionts, several sugar- and amino acid-transporter genes were specifically upregulated during symbiosis establishment 30. Nine DEGs possibly involved in transport were upregulated in Smic-inoculated larvae (Supplementary Figure S4), as were one that contributes to cell volume homeostasis (SLC12A6: aten_s0482.g4) and two that may transport sugars or amino acids (SLC2A12: aten_s0153.g34, SLC16A3: aten_s0261.g16), suggesting that these may be needed to adjust intercellular conditions during initial contact with native symbionts. In addition, in the previous study, two genes, aten_s0153.g34 (SLC2A12) and aten_s0482.g4 (SLC12A6), were also upregulated at 4 dpi 30, suggesting their importance during the transition to symbiosis.
On the other hand, 20 categories of UniProt keywords were exclusively observed among downregulated DEGs at 24 hpi (Table 2). In these categories, transcription and translation (RNA-mediated gene splicing, rRNA processing, ribosome biogenesis, chromosome partition, DNA condensation, nonsense-mediated mRNA decay, and protein biosynthesis), cell proliferation (cell cycle, differentiation, DNA recombination, and myogenesis), bulk transport (endocytosis and exocytosis), and immune response (apoptosis and immunity) were included (Table 2).
DEGs related to immunity and apoptosis.
It is well known that the immune system is modulated during symbiosis establishment in sea anemones 18, 31, 32. Four genes (NLRC4: aten_s0069.g42, aten_s0501.g7 and aten_s0600.g1; MFHAS1: aten_s0098.g22) possibly involved in immunity were significantly downregulated in Smic-inoculated samples at 24 hpi, and one gene (MYD88: aten_s0026.g123) was downregulated in Stri-inoculated larvae at 1 hpi (Figure 3). Apoptosis plays a major role in the host immune response to invading microbes 33. 11 genes (NLRC4: aten_s0069.g42, aten_s0501.g7 and aten_s0600.g1; ACIN1: aten_s0241.g45; TAXBP1: aten_s0117.g27; ZC3H8: aten_s0084.g88; DIDO1: aten_s0077.g2; PIDD1: aten_s0357.g5 and aten_s0037.g33; SLK: aten_s0042.g77: TRAF4: aten_s0001.g189) involved in apoptosis were exclusively downregulated in Smic-inoculated larvae at 24 hpi (Figure 3).
DEGs related to symbiont recognition and phagocytosis.
The initial interaction with algal symbionts must involve pattern recognition 3. Lectin-like genes are important to identify glycans on surfaces of symbionts 15. We identified 306 genes with lectin-like domains from the A. tenuis genome (Supplemental Data S1) and found that four genes (aten_s0084.g103; aten_s0074.g41; aten_s0026.g131; aten_s0023.g63) were exclusively differentially expressed in Smic-inoculated larvae (Figure 4). Of those, three genes (aten_s0074.g41, aten_s0026.g131 and aten_s0023.g63) were predicted to be localized on the cell membrane by DeepLoc, a deep learning neural networks model. Endocytosis, including phagocytosis, is the main cellular mechanism to uptake symbionts 3. Among genes involved in this process, one (STAB2: aten_s0096.g129) was upregulated, but three genes (FKBP15: aten_s0162.g6; EPS15: aten_s0079.g89; MYO6: aten_s0018.g47) were downregulated in Smic-inoculated larvae (Supplementary Figure S5). One gene (LRP4: aten_s0033.g2) was downregulated in all three samples, and one gene (APP: aten_s0027.g17) was exclusively downregulated in Stri-inoculated larvae (Supplementary Figure S5). On the other hand, two genes (UNC13B: aten_s0106.g44l; MIA3: aten_s0223.g30) involved in exocytosis were significantly downregulated in Smic-inoculated samples (Supplementary Figure S5).
DEGs possibly controlling gene expression for establishment of coral-algal symbiosis.
In order to identify genes that may govern coral-algal symbiosis, we focused on signal molecules and transcription factors among DEGs. While eight genes (HLF: aten_s0063.g61 and aten_s0156.g13; TEF: aten_s0156.g11; ETS-2: aten_s0128.g47; HES4: aten_s0026.g27; ZNF271: aten_s0028.g32; CIC: aten_s0075.g3; GCM2: aten_s0286.g9) with transcription factor domains were detected as DEGs, no genes with signaling domains were detected (Supplementary Table S4). These genes were not differentially expressed during symbiosis establishment with native symbionts 30, indicating that they may control the drastic changes in gene expression during initial contact with native symbionts.