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I Supplementary Information For: 1 2 Tripartite Holobiont 1 Supplementary Information for: 2 3 Tripartite holobiont system in a vent snail broadens the concept of chemosymbiosis 4 5 Yi Yang1, Jin Sun1, Chong Chen2, Yadong Zhou3, Yi Lan1, Cindy Lee Van Dover4, 6 Chunsheng Wang3,5, Jian-Wen Qiu6, Pei-Yuan Qian1* 7 8 * Corresponding author: Pei-Yuan Qian 9 Email: [email protected] 10 11 12 This PDF file includes: 13 14 Figures S1 to S13 15 Tables S1 to S3 16 Supplementary Note 1 to Note 9 17 Legends for Datasets S1 to S4 18 SI References 19 20 Other supplementary materials for this manuscript include the following: 21 22 Datasets S1 to S4 23 I 24 Table of Contents 25 Supplementary Figures ........................................................................................................... 1 26 Figure S1. AED score distribution deduced from all of the gene models. ............................ 1 27 Figure S2. Unique orthologous genes of the Wocan Alviniconcha marisindica based on 28 genomic comparisons with the other three Lophotrochozoa ................................................. 2 29 Figure S3. Gill endosymbionts and intestinal ectosymbionts of Alviniconcha marisindica 30 from the Wocan vent field ..................................................................................................... 3 31 Figure S4. Genomic comparisons and gene family analyses of the Wocan Alviniconcha 32 marisindica endosymbiont and the other four campylobacterotal close relatives ................. 4 33 Figure S5. DNA-repair genes in representative Proteobacteria ............................................. 5 34 Figure S6. The abundance of the symbionts in gill and intestine of snail Alviniconcha 35 marisindica ............................................................................................................................ 6 36 Figure S7. Pan-genome of 23 Alviniconcha marisindica endosymbionts from the Wocan 37 vent field ................................................................................................................................ 7 38 Figure S8. Genome-based comparisons of 23 endosymbiotic isolates of Alviniconcha 39 marisindica from the Wocan vent field ................................................................................. 8 40 Figure S9. Transcriptional activity of genes participating in tripartite syntrophic 41 interactions in the Wocan Alviniconcha marisindica holobiont ............................................ 9 42 Figure S10. Nutrient biosynthesis capability of the Wocan Alviniconcha marisindica 43 holobiont .............................................................................................................................. 10 44 Figure S11. Transcriptional activity of genes participating in the nutrient digestion and 45 absorption of the Wocan Alviniconcha marisindica host and bacterial immune evasion and 46 defence ................................................................................................................................. 11 47 Figure S12. Gene Ontology (GO) enrichment network of differentially expressed genes 48 (DEGs) ................................................................................................................................. 12 49 Figure S13. Bathymetric map of the hydrothermal vents over Central Indian Ridge and 50 Carlsberg Ridge.. ................................................................................................................. 13 51 Supplementary Tables ........................................................................................................... 14 52 Table S1. The BUSCO score for different version of the assembly. ................................... 14 53 Table S2. Quast genome assembly assessment report of Alviniconcha marisindica. ......... 15 54 Table S3. The annotation and expression levels of genes involved in encoding 55 representative exo-hydrolases in intestinal flora of three Alviniconcha marisindica 56 individuals. ........................................................................................................................... 16 57 Supplementary Notes ............................................................................................................. 21 58 Supplementary Note 1 ....................................................................................................... 21 59 Figure S14. A photograph of snail Alviniconcha marisindica collected from the WHF 60 which stored in absolute ethanol. Scale bar = 10 cm. ...................................................... 22 61 Figure S15. SEM images of radula. ................................................................................. 23 62 Figure S16. Scatter plot of shell width (diameter) vs. shell height across a size range of 63 19 specimens from Alviniconcha snails ........................................................................... 24 64 Table S4. Shell parameters of Alviniconcha marisindica ................................................ 24 65 Figure S17. Molecular taxonomy of the population of Alviniconcha snails from Wocan 66 vent site on Carlsberg Ridge ............................................................................................ 26 67 Supplementary Note 2 ....................................................................................................... 26 68 Table S5. The nucleic acid preparation and Illumina paired-end sequencing information 69 of different tissues/organs from 16 Alviniconcha marisindica individuals in this study. 28 70 Table S6. The PacBio and ONT sequencing information of DNA from one Alviniconcha 71 marisindica individual for holobiont genome assembly. ................................................. 31 72 Supplementary Note 3 ....................................................................................................... 31 73 Figure S18. A 17-mer histogram for the Alviniconcha marisindica genome. ................ 31 II 74 Table S7. The statistics of the genome assembly. The number in bold indicates the best 75 among all of the assemblers. ............................................................................................ 32 76 Table S8. Information of the bacterial sequences removed from the assembled host 77 contigs. ............................................................................................................................. 33 78 Supplementary Note 4 ....................................................................................................... 33 79 Table S9. The classified repeat content in the genome. ................................................... 33 80 Table S10. Lophotrochozoan genomes that were used for the phylogeny and gene family 81 analyses. ........................................................................................................................... 36 82 Figure S19. Genome-based phylogeny of selected taxa showing the position of the 83 Alviniconcha marisindica among lophotrochozoans. ...................................................... 37 84 Table S11. The time constrain that was applied to calibrate the species divergent time in 85 the MCMCTree analysis. ................................................................................................. 37 86 Supplementary Note 5 ....................................................................................................... 38 87 Figure S20. The maximum likelihood (ML) phylogenetic tree of endosymbionts of 88 Alviniconcha snails and other marine bacteria based on 16S rRNA gene.. ..................... 38 89 Table S12. The general genomic features of A. marisindica symbionts. ........................ 40 90 Figure S21. The overview of genome of Mollicutes symbiont in the gill of A. 91 marisindica constructed using GView Server.. ............................................................... 40 92 Supplementary Note 6 ....................................................................................................... 41 93 Supplementary Note 7 ....................................................................................................... 43 94 Figure S22. Genomic comparison analysis across representatives of Campylobacterota. 95 .......................................................................................................................................... 43 96 Supplementary Note 8 ....................................................................................................... 45 97 Supplementary Note 9 ....................................................................................................... 45 98 Figure S23. Gene Ontology (GO) functional annotations of highly expressed genes in 99 the digestive gland, foot, gill, and intestine.. ................................................................... 46 100 Figure S24. Differentially expressed genes (DEGs) in the intestine and gill of 101 Alviniconcha marisindica.. .............................................................................................. 47 102 Figure S25. Transcriptional activity of genes participating in the globin of Wocan 103 Alviniconcha marisindica for substrates transportation.. ................................................. 48 104 Dataset S1 (separate file). The annotation and expression levels of genes involved in 105 encoding hydrolases in intestinal flora of three A. marisindica individuals. ........................... 49 106 Dataset S2 (separate file). The annotation of genes predicted from the metagenome of 107 intestinal flora from three snail individuals.
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