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. Tragin, Ocean Sampling Day: 18S V4 vs V9 comparison, p.23

S. Fig and . S1, Bioinformatics pipeline use to build and assigned OTUs from V4 and V9 628 datasets. Reference alignment was SILVA seed release 119. The Chlorophyta curated PR² database 629 (Tragin et al., 2016) was used as taxonomic reference. The number of sequences at each step appears in 630

S. Fig, S2: A. Rarefaction curves; B. Rank abundance distribution. x-axis represents OTUs 632 by decreasing number of sequences

S. Fig and B. S4:-a, Non-metric Multi Dimensional Scaling (NMDS) representation of 635 communities based on lowest taxonomic level (OTUs) for V4 (A) and V9 (B). The dissimilarity matrix 636 was computed using Bray Curtis distance

S. Fig, S5: Correlation between V4 and V9 relative contribution to photosynthetic 640 metabarcodes in major photosynthetic phyla, A. Ochrophyta. B. Chlorophyta. C. Haptophyta. D

S. Fig, S7: Percentage of genera from photosynthetic groups found either only in V4 (blue), 646 or only in V9 (red), or in both datasets (grey) Only taxonomically valid genera and only Classes with 647 at least 5 genera were taken into account

S. Fig, S8: Correlation between V4 and V9 relative contribution to photosynthetic 650 metabarcodes for major Chlorophyta classes, A. Mamiellophyceae. B. Trebouxiophyceae. C

B. Chlorophyta-classes, Mamiellophyceae genera. The colors correspond to the difference from -50% (- 655 0.5)

. Tragin, Ocean Sampling Day: 18S V4 vs V9 comparison, p.25

M. Booth and B. North, Atlantic Ocean East coast of USA 290 311 69

L. Rocha and N. South, Atlantic Ocean Coast of Uruguay