FIG 3.

Sequence variability of the trichostome 18S rRNA gene. Sequence variability is expressed as the Shannon index for each alignment position of the 126 aligned trichostome ciliate sequences (black circles). Shannon indices for a subset of 54 aligned sequences from genera known to occur in the rumen are shown in gray circles. The sequence of Balantidium entozoon was omitted because it was shorter than all other remaining reference sequences. A 20-bp moving average was used. Approximate positions of frequently targeted variable regions (V2 to V9) for community structure analysis are shown for orientation. Labeling of variable regions corresponds to eukaryotic 18S rRNA gene variable region designations (75). V6 is highly conserved among eukaryotes in general and therefore indistinct (76). Nucleotide numbering corresponds to base positions in the Saccharomyces cerevisiae strain NCYC 505 18S rRNA gene (GenBank accession number Z75578).