Fig 1.

Position of intervening sequences in the 23S rRNA gene. (A) The orange Guaymas Beggiatoa genome sequence includes a single set of rRNA genes. The figure combines JGI and RAST annotations; the 23S rRNA gene was not annotated by JGI and therefore has no number. It contains putative intron and homing endonuclease insertions, separated by 14 bp of apparent rRNA sequence. The intron sequence overlaps the upstream portion of the 23S gene by 4 bp. (B) The orange Guaymas Beggiatoa intervening sequences are in the predicted helix 69 loop and between helices 69 and 71 of the predicted rRNA structure, a region in which a variety of other bacteria and archaea also harbor putative introns and homing endonucleases, as outlined in the figure. These were identified primarily by searching the Silva (75) LSURef 111 database for 23S rRNA gene sequences longer than 3,000 bp and refining the alignment to place the intervening sequences precisely.