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Method used for targeted metagenomic sequencing of Prochlorococcus and Synechococcus for environmental and culture samples (Fig. S1), outcomes of different cell lysis treatments (Fig. S2), mean coverage depth for genomic regions defined by GC content (Fig. S3), relationship between the replicated samples for each bulk environmental genomic DNA and sorted Synechococcus transposon sample not normalized to the same number of matched sequences (Fig. S4), location, sampling date and corresponding environmental and sequencing values of samples analyzed (Table S1), details of the data set used based on sequencing values (Table S2), phosphate and nitrogen acquisition gene sequences (Table S3), and GenBank accession numbers (Tables S4 and S5).
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