Additional file 1 of Pervasive tandem duplications and convergent evolution shape coral genomes
Creators: name: Noel, Benjamin
name: Denoeud, France
name: Rouan, Alice
name: Buitrago-López, Carol
name: Capasso, Laura
name: Poulain, Julie
name: Boissin, Emilie
name: Pousse, Mélanie
name: Da Silva, Corinne
name: Couloux, Arnaud
name: Armstrong, Eric
name: Carradec, Quentin
name: Cruaud, Corinne
name: Labadie, Karine
name: Lê-Hoang, Julie
name: Tambutté, Sylvie
name: Barbe, Valérie
name: Moulin, Clémentine
name: Bourdin, Guillaume
name: Iwankow, Guillaume
name: Romac, Sarah
name: Agostini, Sylvain
name: Banaigs, Bernard
name: Boss, Emmanuel
name: Bowler, Chris
name: de Vargas, Colomban
name: Douville, Eric
name: Flores, J. Michel
name: Forcioli, Didier
name: Furla, Paola
name: Galand, Pierre E.
name: Lombard, Fabien
name: Pesant, Stéphane
name: Reynaud, Stéphanie
name: Sullivan, Matthew B.
name: Sunagawa, Shinichi
name: Thomas, Olivier P.
name: Troublé, Romain
name: Thurber, Rebecca Vega
name: Allemand, Denis
name: Planes, Serge
name: Gilson, Eric
name: Zoccola, Didier
name: Wincker, Patrick
name: Voolstra, Christian R.
name: Aury, Jean-Marc
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology

description: Additional file 1: Table S1. Statistics of the ONT sequencing data. Table S2. Raw long-read assemblies. A. Porites lobata. B. Pocillopora cf. effusa. Table S3. Statistics of all assemblies.  Table S4. Statistics of gene prediction on reference and alternative haplotype assemblies. Table S5. BUSCO analyses of raw and haploid assemblies. Table S6. Repeat composition of coral assemblies. Table S7. Data used for comparison of 26 Cnidaria species. Table S8. Coverage of genome assemblies by syntenic blocks (for contigs with at least 5 genes). Table S9. Validation of pairs of adjacent duplicate genes and clusters of tandemly duplicated genes. Table S10. Table of calcification-related proteins in non-scleractinian and scleractinian - robust and - complex coral species. Figure S1. K-mer distribution and estimation of genome sizes and heterozygous rates from short reads. Figure S2. KAT plot of Porites lobata assemblies. Figure S3. KAT plot of Pocillopora cf. effusa assemblies. Figure S4. K-mer profiling for all assemblies of Porites lobata and Pocillopora cf. effusa  Figure S5. Distribution of the number of genes in tandemly repeated gene clusters. Figure S6. Validation of pairs of adjacent duplicated genes and clusters of TDG. Figure S7. Validation of pairs of adjacent duplicated genes. Figure S8. Validation of TDG clusters. Figure S9. Comparison of haplotype assemblies and annotations for a TDG cluster.  Figure S10. Two P. lobata genomic regions that illustrate proteins and transcripts alignments before or after the adaptation of gene prediction workflow for tandemly duplicated genes. Figure S11. Consensus sequences of palindromic ITS satellites, found in Porites lobata, Porites evermanni and Porites lutea genomes. Figure S12. Conservation of orthologous genes in Porites lobata and Pocillopora cf. effusa with other Cnidarian.  Figure S13. Number of TDG genes vs total number of genes on contigs. Figure S14. Expanded PFAM domains in corals vs non-corals hexacorallia. Figure S15. OGs amplified in complex vs robust corals. Figure S16. Expanded PFAM domains in complex vs robust corals. Figure S17. OGs amplified in massive vs branched corals.  Figure S18. Heatmap representing the P-values obtained with CAFE for gene number amplification and reduction events for each node on the phylogenetic tree. Figure S19. Gene family amplifications/reductions identified with CAFE.  Figure S20. Distribution of Ks between TDG gene pairs in four classes of intergenic distances. Figure S21. View of the Pocillopora cf. effusa genome browser, with 2 adjacent genes duplicated in tandem. Figure S22. Distribution of Ks between TDG pairs in 3 structural conservation classes. Figure S23. View of a cluster of 3 tandemly duplicated genes belonging to OG0000023 (lectin-like domain). Figure S24. Expression quantification of 200 random OGs across the 103 meta-transcriptome samples. Figure S25. Number of genes in OG identified as TLR, NLR and lectins. Figure S26. Percent of NACHT/NB-ARC containing proteins that are likely truncated at the N-terminal, C-terminal or both extremities. Figure S27. Observed N-terminal and C-terminal domains for NACHT/NB-ARC containing proteins in five coral species. Figure S28. Graphic representation of the number of calcification-related proteins in non-scleractinian and scleractinian species and associated p-values. Figure S29. Maximum likelihood phylogenetic tree of cnidarian ammonium transporters Amt1. Figure S30. Genomic localisation of cnidarian ammonium transporters Amt1 in various species. Figure S31. Genomic localisation of Bicarbonate Anion Transporter SLC4 in various species. Figure S32. Coral monocopy gene set.