Supplementary Materials

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

Senjie Lin, Shifeng Cheng, Bo Song, Xiao Zhong, Xin Lin, Wujiao Li, Ling Li, Yaqun Zhang, Huan Zhang, Zhiliang Ji, Meichun Cai, Yunyun Zhuang, Xinguo Shi, Lingxiao Lin, Lu Wang, Zhaobao Wang, Xin Liu, Sheng Yu, Peng Zeng, Han Hao, Quan Zou, Chengxuan Chen, Yanjun Li, Ying Wang, Chunyan Xu, Shanshan Meng, Xun Xu, Jun Wang, Huanming Yang, David A. Campbell, Nancy R. Sturm, Steve Dagenais-Bellefeuille, David Morse

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S13
  • References
Tables S1 to S35
Table S1. Features of sequencing libraries (insert size between 170bp and ~20Kb) and statistics of the sequencing data (post-filtering clean data). In total, 151 Gb clean data was produced with a resulting sequencing depth of 130X.

Table S2. Summary statistics of k-mer analysis and resulting genome size estimates in S. kawagutii.

Table S3. Genome assembly evaluation by mapping gene regions to transcriptome sequences. Transcriptome data (EST sequences) were collected from three cDNA libraries sequenced using Sanger (12,990 high-quality long reads) and 454 (834,546 high-quality reads) sequencing techniques, which were merged and clustered into a set of 70,985 unique genes. This table describes the alignment results between the 70,985 unigenes and the gene regions of our genome assembly.

Table S4. Genome assembly evaluation by mapping fosmid clones to scaffolds.

Table S5. General genome profile in S. kawagutii in comparison to the eukaryotes S. minutum, P. falciparum, P. tricornutum and A. thaliana.

Table S6. Tandem array genes and their InterPro functional annotation in the S. kawagutii genome.

Table S7. Enzymes and their corresponding gene IDs for the major metabolic pathways in the assembled S. kawagutii genome.

Table S8. Genes annotated as potentially involved in sexual reproduction, sporulation (cyst formation and germination) and telomere synthesis in the assembled S. kawagutii and S. minutum genomes (numbers indicate copy numbers).

Table S9. Gene families gained in the ancestor of Symbiodinium.

Table S10. The enriched ontologies of gene families gained in the ancestral Symbiodinium.

Table S11. Gene families that have shrunk in Symbiodinium spp.

Table S12. Gene families expanded in Symbiodinium spp.

Table S13. An example of duplicated genomic blocks within S. kawagutii genome and the associated functional annotation. Overall, duplicated segments within S. kawagutii are rare; here we give the most notable syntenic blocks in the genome detected by Mcscan method (http://chibba.agtec.uga.edu/duplication/mcscan/) using genes as anchors (-e_value: 1e-5; -match_size=5).

Table S14. Statistics of repeat elements annotated in S. kawagutii genome.

Table S15. Domains linked to transposable elements in S. kawagutii and six other species. All domain information was annotated by the Pfam package; here we focus on"Reverse transcriptase", "Integrase" , "C-5 cytosine methyltransferase", "Zinc finger (Znf)", and their connections (links) within genes. S. minutum, Symbiodinium minutum; P. marinus, Perkinsus marinus (perkinsid); P. falciparum, Plasmodium falciparum (apicomplexan); P. tetraurelia, Paramecium tetraurelia (ciliate); P. tricornutum, Phaeodactylum tricornutum (diatom); A. thaliana, Arabidopsis thaliana (land plant).

Table S16.S. kawagutii genes containing a DinoSL (dinoflagellate-specific spliced leader) in their 5' UTR. In total, we identified 5,568 genes with partial or full SL. Here, we list the 62 genes with full length DinoSL at their 5' UTR, of which 28 (shaded by
orange) contain canonical SL sequence while the others have SLs with 1-3 nucleotides variant.

Table S17. Putative horizontal gene transfer (HGT)-derived genes detected in the S. kawagutii genome. See Supplementary material for methodology used.

Table S18. Collinear blocks between S. kawagutii and S. minutum genomes identified by Mcscan (http://chibba.agtec.uga.edu/duplication/mcscan/) (-e_value: 1e-5; - match_size=5).

Table S19. Statistics of clean S. kawagutii reads aligned to two Symbiodinium genomes. PE, paired end; SE, single end.

Table S20. GO slim categorization of S. kawagutii and S. minutum genes.

Table S21. Summary of copy numbers for genes related to nutrient acquisition and utilization, and metabolite transport in S. kawagutii and other organisms. P. tricornutum, Phaeodactylum tricornutum (diatom); T. pseudonana, Thalassiosira pseudonana (diatom); C.reinhardti, Chlamydomonas reinhardtii (green alga); O. tauri, Ostreococcus tauri (green alga); C. merolae, Cyanidioschyzon merolae (red alga); C.crispus, Chondrus crispus (red alga); E.siliculosus, Ectocarpus siliculosus (brown alga); P. falciparum, Plasmodium falciparum (apicomplexan); A. thaliana, Arabidopsis thaliana (land plant).

Table S22. Summary of copy numbers for genes related to antioxidant and anti-stress in S. kawagutii and other organisms. P. tricornutum, Phaeodactylum tricornutum (diatom); T. pseudonana, Thalassiosira pseudonana (diatom); C.reinhardti, Chlamydomonas reinhardtii (green alga); O. tauri, Ostreococcus tauri (green alga); C. merolae, Cyanidioschyzon merolae (red alga); C.crispus, Chondrus crispus (red alga); E.siliculosus, Ectocarpus siliculosus (brown alga); P. falciparum, Plasmodium falciparum (apicomplexan); A. thaliana, Arabidopsis thaliana (land plant).

Table S23. Clusters of conserved promoter motifs. Symbols for degenerate positions are shown at right.

Table S24. Pre- and mature miRNA sequences (those highlighted in green were used to design probes for RNA blot hybridization).

Table S25. Target genes of miRNA in S. kawagutii genome (those targeted by highly expressed miRNAs are highlighted in yellow).

Table S26. The enriched ontologies of genes potentially targeted by miRNAs in the S. kawagutii genome.

Table S27. The enriched ontologies of genes potentially targeted by highly expressed miRNA in the S. kawagutii genome.

Table S28. Protein-protein interaction networks of S. kawagutii miRNA targets based on networks from Arabidopsis thaliana and Saccharomyces cerevisiae. In red are miRNA target genes detected in the coral Acropora digitifera.

Table S29. Genes in the coral A. digitifera (Acropora digitifera) computationally predicted to be targets of S. kawagutii miRNA.

Table S30. The enriched ontologies of genes potentially targeted by miRNAs in the A. digitifera genome.

Table S31. N-Glycan biosynthetic enzymes in the genomes of Symbiodinium and other algae as well as transcriptomes of two other dinoflagellates. K. veneficum, Karlodinium veneficum (dinoflagellate); A. carterae, Amphidinium carterae (dinoflagellate); O. tauri, Ostreococcus tauri (green alga); P. tricornutum, Phaeodactylum tricornutum (diatom); M. pussila, Micromonas pussila (green alga); E. huxleyi, Emiliania huxleyi (haptophyte).

Table S32. Genes possibly involved in symbiosis (numbers indicating copy numbers) unique to Symbiodinium (compared with nine other eukaryotes representing plants, algae, cnidarian, and Apicomplexa) or only shared with the apicomplexan parasite Plasmodium (shaded in pink). Phosphoadenosine phosphosulfate reductase, calumenin and phosphatidylinositol-3-phosphate kinase are exceptions that are shared with several other organisms despite being previously proposed to be involved in symbiosis (Davy et al. 2012; ref 22). Species bbreviations: A_thaliana, Arabidopsis thaliana (land plant ); C_crispus, Chondrus crispus (red macroalga); C_merolae, Cyanidioschyzon merolae (unicellular red alga); C_reinhardtii, Chlamydomonas reinhardtii (green alga); E_siliculosus, Ectocarpus siliculosus (brown alga); O_tauri, Ostreococcus tauri (green alga); P_falciparum, Plasmodium falciparum (apicomplexan parasite); P_tricornutum, Phaeodactylum tricornutum (diatom); T_pseudonana, Thalassiosira pseudonana (diatom); S_kawagutii, Symbiodiniumkawagutii; S_minutum, Symbiodinium minutum.

Table S33. Major S. kawagutii and A. digitifera (coral) genes potentially involved in symbiosis and likely direction of action of the encoded products in the presumed pair of these two organisms.

Table S34. Transporters identified from Symbiodium genomes compared with those in related organisms. S. kawagutii, Symbiodinium kawagutii; S. minutum, Symbiodinium minutum; A. digitifera, Acropora digitifera (coral); K. veneficum, Karlodinium veneficum (dinoflagellate); A. carterae, Amphidinium carterae (dinoflagellate); P. tricornutum, Phaeodactylum tricornutum (diatom); T. pseudonana, Thalassiosira pseudonana (diatom).

Table S35. Genes in the genomes of both Acropora digitifera (coral) and S. kawagutii (symbiont) that can potentially be involved in symbiotic material exchange and collaborative combat against stressors. Comparison to the genomes of Hydra magnipapillata and Nematostella vectensis is also shown. The symbiont genes in red are computationally predicted to be plasma membrane proteins. Gene copies located next to one other in the genome are underlined. Light blue shading depicts absence of the gene.