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Additional file 8: Figure S6. Bin reciprocity. Sankey plot depicting MyCC bin correspondence across Illumina and hybrid assembly files (Illumina PE + 1Df or 2D) and their taxonomy/origin in the Caulerpa ashmeadii holobiont based on COGs. Flow size linking bins represent the number of common scaffolds in the assembly files compared via reciprocal BLASTn. Numbers adjacent to bins represent the number of COGs reported by MyCC. Note the consistent delimitation of nuclear contigs but some instability in the binning of the Phyllobacteriaceae sp. and Rhodospirillaceae sp2. scaffolds. The Sankey diagram was built on the basis of html code available from Google Charts at https://developers.google.com/chart/interactive/docs/gallery/sankey. PE = Illumina Paired-Ends scaffolds, PE+1Df = hybrid 1Df scaffolds, PE+2D = hybrid 2D scaffolds.

Additional file 4: Figure S2. Assembly file content. Contig/scaffold abundance per genomic compartment across nanopore and hybrid assemblies. Bubble size represent the percentage of uniquely mapped reads to a given assembly and corresponding dataset (those representing

Additional file 6: Figure S4. Circular Mitochondrion genome map.

Additional file 2. Supplementary tables.

Additional file 9: Figure S7. Metagenome binning. Comparison of delimited bins with MyCC (4mer) for three assemblies. (a) Experimental binning of Canu 1Df contigs. (b) Binning of Spades’ hybrid Illumina+1Df assembly. (c) Binning of Spades’ Illumina-only assembly. Bins containing nuclear and repeat contigs are emphasized with dashed circles. Remaining bins correspond to bacterial taxa. Note that printed bin numbers are unrelated between plots.

Additional file 12: Figure S10. BLASTn report for atp1/atpA. BLASTn alignment of mitochondrial atp1 and chloroplast atpA. Note identity level nearing ~ 70%, causing mismapping of low quality atpA reads on atp1.

Additional file 7: Figure S5. GenomeScope profile. Kmer coverage and log coverage for the entire Illumina dataset (a and b), the dataset depleted of bacterial reads (c and d), and the dataset depleted of nuclear reads (e and f). Note the drop in kmer frequencies indicated by arrows and circles to point at the depletion of bacterial kmers overlapping with nuclear ones (a and c) and their recovery in the dataset depleted of nuclear reads (e). Note as well the successful depletion of the main bacterial kmer peak (*) in the bacterial depleted dataset (a and e vs. c).

Additional file 11: Figure S9. Polished quality of protein-encoding gene. Detailed distributions of gene quality following polishing steps as (a) boxplot or (b) violin plot. For comparison, numbers reported between parenthesis in Table 4 correspond to the cumulative percentage identity, indels and substitutions for all genes, while the data points and distribution in the present figure represent individual gene values. Note the perfect quality of chloroplast genes following Pilon polishing. CP_1DF=Chloroplast genes from 1Df assembly, CP_2D = Chloroplast genes from 2D assembly, MT_1Df = Mitochondrion genes from 1Df assembly.

Additional file 17: Figure S15. BLASTp report for ORF7, ORF8, and ORF9.

Additional file 15: Figure S13. Chloroplast genome long reads’ pile-up.

Additional file 16: Figure S14. BLASTp report for psbA intronic ORFs.

Additional file 10: Figure S8. Phylogeny of valyl-tRNA ligase. Exploratory phylogeny of valyl-tRNA ligase (COG0525) amino acid sequences extracted from nuclear and bacterial bins by MyCC. For taxonomic identification of bins, sequence context was retrieved via BLASTp against GenBank’s non-redundant protein databases. Note the occurrence of two different valyl-tRNA ligases in Caulerpa ashmeadii nuclear genome.

Additional file 5: Figure S3. Circular Chloroplast genome map.

Additional file 14: Figure S12. Error rate vs. assembly. Impact of Canu’s error rate parameter on assembly of the circular chloroplast genome in the presence of structural variation (SV) (black bubbles). Note the occurrence of misassemblies (i.e. polymorphism/SVs stitched on the contig’s extremities) when using relaxed error rates with 2D data, while 1D assembly still produces a circularizable contig (i.e. no misassembly).

Additional file 3: Figure S1. Read length distribution. Density plot depicting read length improvement following decontamination of low molecular weight fragment (LMW). LibRAW: original DNA extract, LibGEL: Gel excised HMW DNA, and LibMAG: HMW DNA selected via 0.4X magnetic bead wash. Data is shown for 1Df and 2D reads. Note the broader shoulder of LibGEL for sequence > 2500 bp.

Additional file 1. FigTree Tutorial and command line usage for TREE2FASTA.

Additional file 5. Illustration of the edited exploratory tree used to measure TREE2FASTA execution speed reported in Table 1. Both trees were edited for color and/or annotation in FigTree for 10 phyla of the tufA and 16S PhytoREF database. Color details: Chlorarachniophyta (CYAN), Chlorophyta (GREEN), Euglenozoa (BLUE), Cryptophyta (BROWN), Rhodophyta (RED), Glaucophyta (MAGENTA), Ochrophyta (ORANGE), Haptophyta (YELLOW), Cyanophyta (BLACK), Streptophyta (PURPLE). Note that smaller phylum clades, albeit present in both trees are not easily visible among other colors (e.g. Cryptophyta, Euglenozoa). Cyanophyta is absent from the PhytoREF. Streptophyta is absent for the tufA database.

Additional file 2. Details of color and annotation information saved within the TAXA block of FigTreeâ s NEXUS file.

Additional file 4. Details of the Florideophyceae clade shown in Fig. 2a.

Additional file 3. Example command line for multiple alignment in MUSCLE and maximum likelihood estimation RAXML to rapidly produce exploratory tree.

Additional file 12: Figure S5. Example of putative index tag jumping or tag error. Comparative read abundance for seven OTUs demultiplexed (i.e. assigned) to both FL02 and JP07. For illustration purpose, only OTUs with >5 % of mapped reads in either FL02 or JP07 are shown (these correspond to seven out of the 141 common OTUs, see Additional file 9: Figure S2). Note the drastic abundance disparity illustrative of or potential of false assignment via index tag jumping or tag error (e.g. OTU 511 representing ≪0.1 % reads in FL02 and 10.4 % of reads in JP07). By contrast, note the more balanced abundance of OTU 355, 356, and 506, which may reflect the true presence of common OTUs in both samples (i.e. pantropical OTUs).

Additional file 13: Figure S6. OTUs vs. clone identity and coverage. Comparison of all phototrophic clones obtained from JP07 with their matching OTUs. Note high identity of clones and OTUs based on 375Â bp, with 0, 1 or 2 base pair variation (100, 99.7 and 99.5Â % respectively). Also note that clone H and its corresponding OTU_364 share the highest coverage, although further cloning would be necessary to accurately assess congruence in sequence coverage between the two methods.

Additional file 5: Table S5. Clone taxonomy. Detailed reference taxonomy for 86 phototrophic clones from microfloras sampled in the Ryukyu archipelago (JP01, JP03, JP04, JP06, JP07, JP25), an aquarium window scrap (E09) and a Gulf of Mexico crustose coralline Lithophyllum sp. rhodolith. Taxonomic groupings with unsettled naming such as combined orders, provisional families, and polyphyletic or monophyletic species or genera complexes, are noted between quotes.

Additional file 7: Table S6. Summary of microfloras richness and abundance at multiple taxonomic levels. (A–B) OTU counts and read abundance for ‘Phototrophs’ vs. ‘Heterotrophs’ group. (C–D) OTU counts and read abundance for phototrophic phyla and classes. (E–F) OTU counts and read abundance for Ulvophyceaen families. Note that OTUs may be found more than once across samples.

Additional file 3: Table S3. Indexed forward primers used for metabarcoding. Indexes in bold.

Additional file 2: Table S2. Barcoded Florideophyceae, Phaeophyceae and miscellaneous taxa. Collection information for specimens of the Florideophyceae and Phaeophyceae sequenced for tufA in the present study (as well as a miscellaneous Prasinophyceae). Polyphyletic orders or family and combined orders are indicated in between quotes. All specimens from shallow waters (0–10 m) otherwise indicated in footnotes. Collector (Coll.) initials as follows: CP = C. Pueschel, CS = C. Stoude, DG = D. Gabriel, DK = D. Krayesky, DWF = D.W. Freshwater, EC = E. Coppejans, ED = E. Deslandes, JC = J. Cabioch, JH = J. Hughey, JR = J. Richards, JRu = J. Rueness, JZ = J. Zertuche, MG = M. Guiry, MHH = M. H. Hommersand, MJW = M. J. Wynne, MY = M. Yoshizaki, OC = O. Camacho, SF = S. Fredericq.

Additional file 4: Table S4. Summary taxonomy and content of the non-redundant tufA database. Diversity and sequence counts for (A) Heterotrophs and Phototrophs, (B) Phyla and Classes for all phototrophs and (C) Orders/suborders and families for the Ulvophyceae (Genus taxonomy not shown for conciseness). Taxonomic groupings with unsettled naming such as combined orders, provisional families, and polyphyletic families (i.e. ‘Kornamanniaceae’ and ‘Ulothrichaceae’) are noted between quotes.

Additional file 8: Table S7. OTUs taxonomy and their microflora assignment. Detailed reference taxonomy for 802 core OTUs as determined from their phylogenetic position (see Fig. 6). Taxonomic groupings with unsettled naming such as combined orders, provisional families, and polyphyletic or monophyletic species or genera complexes, are noted between quotes.

Additional file 1: Table S1. Barcoded Ulvophyceae. Collection information for Ulvophyceae specimens newly sequenced for tufA. To ease public database searches, Genbank® identifiers include both morphological and molecular identification (in brackets []) at the genus or family level (when abbreviated). Polyphyletic genera, species complexes or combined orders indicated in between quotes. All specimens from shallow waters (

Additional file 1: Table S1. Barcoded Ulvophyceae. Collection information for Ulvophyceae specimens newly sequenced for tufA. To ease public database searches, Genbank® identifiers include both morphological and molecular identification (in brackets []) at the genus or family level (when abbreviated). Polyphyletic genera, species complexes or combined orders indicated in between quotes. All specimens from shallow waters (