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Table 3 PCR and sequencing results for environmental 18S rRNA gene amplicons

From: Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution

Strain/sample NSF83-1528R Diphy257F-Diphy1881R Diphy453F-1528R PacBio sequences CCS = 1 OTUs Diphyllatea OTUs
Freshwater DNA
 Årungen Y Y 16 4 4 (2, 14)
 BOR41 Y Y 396 43 6 (2, 40)
 BOR42 Y Y 20 4 4 (1, 17)
 BOR43 Y Y 525 9 3 (1, 12)
 LD_DERW20 Y N N
 LD_ESTH20 Y N Y 16 8
 LD_BASS2, 20 Y N Y 14 10
 SA78, 81 Y N Y 9 7
Marine DNA
 NB038 Y N Y 248 115
 RA119 Y N Y 232 54
 VA105 Y N N
 2OF268 Y N Y 54 23
  1. Y = PCR product, N = no PCR product. The value for the PacBio reads (column five) is minus chimeras identified in Uchime. For Diphyllatea OTUs (last column) the number in brackets represents firstly the number of OTUs constituting > 1 read, and secondly the total number of reads these non-unique OTUs constitute; these are represented in the rRNA phylogeny (Fig. 3 and Additional file 1: Figure S2). For additional sequencing results per PacBio barcode see Additional file 1: Table S2. The total diversity of all 281 OTUs generated in this study is provided in Additional file 1: Figure S4. Though briefly, and outside the scope of this study, for the marine samples (192 OTUs): bivalve, ciliate, diatom, dinoflagellate and segmented worm rRNA were most abundant. For the freshwater samples (25 OTUs): ciliate, cryptomonad and diatom rRNA were most common