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Table S3 Mean protein sequence similarities of transcripts to the genes in its reference genome. Values are displayed for taxa within phylogenetic orders that contain more then 5 taxa and the pool of all transcripts assigned to taxa with ≥ 2,000 transcripts in each of the treatments in one of the experiments. Similar mean values for protein sequence similarities among orders and the complete dataset indicate that the quality of transcript assignment to taxa was not biased among phylogenetic orders. Phylogenetic order Mean sequence similarity (± standard deviation) Alteromonadales 87.9 ± 10.6 Oceanospirillales 87.8 ± 12.4 Pseudomonadales 80.7 ± 13.0 Rhodobacterales 85.7 ± 11.9 All taxa ≥ 2,000 transcripts 86.9 ± 11.6