jpy12055-sup-0001-FigS1.pdfapplication/PDF48KFigure S1. Sequence evidence indicating that the axenic strains are clonal. (A) A 569-bp segment of cp23S was amplified by PCR from strain SSB01 and sequenced repeatedly from separate E. coli colonies as described in the text. Forty-one colonies yielded the identical consensus sequence (top line), whereas eight colonies yielded sequences that differed from the consensus by one (lines 2–8) or three (line 9) single nucleotides in the positions shown by the small hatch-marks. Nine colonies yielded sequences that differed from the consensus by a six-nucleotide deletion (lines 10 and 11, large hatch-marks; the same deletion in each case); in one of these cases there was also an additional single-nucleotide difference from the consensus (line 11). All of these variations seem most likely to represent PCR errors, sequencing errors, and/or intragenomic variation, as discussed in the text. Similar results were obtained with strains SSA02 (83 clones sequenced), SSA03 (34 clones sequenced), SSE01 (27 clones sequenced), and SSF01 (27 clones sequenced), except that none of these strains displayed anything like the 6-nucleotide deletion observed in some of the SSB01 sequences; instead, only single-nucleotide differences from the respective consensus sequences were observed, and none of these was observed more than once. (B) An analysis identical to that in A was performed on DNA from Aiptasia strain H2, the original host for SSB01. The results were essentially identical to those with SSB01.
jpy12055-sup-0002-FigS2.pdfapplication/PDF935KFigure S2. Nucleotide-sequence alignment of cp23S Domain V in the five axenic Symbiodinium strains. Dots represent nucleotides conserved among three or more strains, dashes represent gaps introduced to optimize the alignment, and nonconsensus nucleotides are indicated.

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