Figure 1:
Secondary structure models for plastid SSU rRNA from: a) Polytoma uvella 964; b) Polytoma obtusum; c) Polytoma mirum; and d) Chlamydomonas humicola. See the Comparative RNA Web Site for more information.
Figure 2:
SSU rRNA sequence alignment in a) GenBank format, b) PHYLIP format, and c) printable version (PostScript and PDF formats) of 3 Polytoma plastid sequences, including comparison to a chloroplast consensus sequence. Five chloroplast sequences (Chlamydomonas humicola, Polytoma 62-27, Polytoma obtusum, Polytoma uvella 964, and Zea mays) were aligned with Escherichia coli and a chloroplast consensus sequence. Sequences were aligned to maximize sequence similarity and to juxtapose positions that are base paired in the comparatively inferred secondary and tertiary structure model (Gutell 1996). Secondary structure information is incorporated into this alignment. Positions with underscores in the helix sequence are involved in secondary or tertiary structure base pairing, while the "~" symbol designates unpaired positions. Deletions in one sequence relative to the others are shown with a dash "-". Positions that are within hairpin loops are enclosed with brackets "()"; vertical bars "|" flank the ends of helices. The chloroplast consensus line (Con.chlor.95%) contains nucleotide positions that are conserved in 95% or more of the 70 aligned chloroplast sequences, and are shown as A, C, G, or U; while positions conserved less than 95% are shown with a "+". In contrast, the C. humicola and the three Polytoma sequences are printed to emphasize their identity to and differences from the 95% chloroplast consensus sequence. Positions identical with this sequence are shown with a period ".", while actual nucleotide letters denote differences from the consensus sequence. Differences between any one of the Polytoma sequences and the 95% conserved positions are shaded. These positions are further analyzed in the diff.95% sequence line. "$" denote positions with compensatory base changes in the comparatively inferred base pairs; "*" denote a single uncompensated base pair substitution between GU and GC or AU; "?" denote all other single uncompensated base pair changes; and "o" denote differences at unpaired positions. The locations of sequences in the Polytoma rRNAs that are presumed to be introns are denoted with the symbol "#". These presumed intron sequences are not included in this alignment, but are available from GenBank (XXXXXXXX, XXXXXXXX, and XXXXXXXX).
Figure 3:
A) Secondary structure comparison of 3 Polytoma leucoplast sequences to a chloroplast consensus secondary structure. The patterns of conservation for the 70 publicly available chloroplast SSU rRNA sequences (B) are superimposed onto the Zea mays chloroplast SSU rRNA secondary structure diagram (Gutell 1994). Four levels of conservation are shown. All of the positions in the Zea mays structure that are present in at least 95% of the chloroplast sequences are shown with either a nucleotide, a closed circle, or an open circle. At the highest level of conservation, nucleotides conserved at greater than (or equal to) 95% are shown with red uppercase letters, nucleotides conserved between 90 and 95% are shown with red lowercase letters. Nucleotides conserved between 80 and 90% are shown as closed circles, while nucleotides conserved in less than 80% are shown as open (and slightly smaller) circles. The two intron sites are denoted with arrows, and the unique insertion in P. uvella is shaded gray. Positions with the symbols "$, *, ?, o" in the "diff.95%" line of the alignment (Figure 2) are identified on this secondary structure diagram. Position numbers for the Zea mays chloroplast (GenBank # Z00028) SSU rRNA sequence are shown for every 50th nucleotide.
Figure 4:
All differences between the rrn16 sequences of P. obtusum and P. uvella 964 at paired and unpaired positions in SSU rRNA secondary structures. The positional differences, shown as solid circles, are superimposed on the P. uvella 964 secondary structure model from Figure 1. GC and AU basepairs are connected with a thin line, GU basepairs with a small closed circle, AG basepairs with a large open circle, and other non-canonical basepairs with a large closed circle, based on the P. uvella structure. The explanation for basepair symbols for positions with variation between the two Polytoma sequences is illustrated in Figure 3. For basepairs that change at both positions, the thick BP line denotes one WC pair exchanged for another, while a large closed circle denotes all other changes (e.g. WC exchanged with a non-canonical). For basepairs that change at only one of the positions, the thick BP line denotes a AU or GC exchange with a GU, while large closed circles are for non-canonical exchanges with WC or other non-canonical pairs.
