Last modified on 30 January 2007.

Table 4: Phylogenetic Distribution

The distribution of introns on the phylogenetic tree is tabulated in Table 4. Table 4A reveals the ratio of the number of rRNA introns per rRNA gene for the nuclear, chloroplast, and mitochondrial encoded RNAs for the major phylogenetic groups. The most noteworthy distributions are: 1) The majority (96%) of the rRNA introns occur in Eucarya, followed by the Archaea, and the Bacteria. 2) Only one rRNA intron hasVery few rRNA introns have been documented in the Bacteria; due to the large number of rRNA gene sequences that have been determined, the ratio of rRNA introns per rRNA gene is essentially zero for the bacteria. 3) The frequency of introns in Archaea rRNAs is higher, with 43 examples documented as of December 2001. Within the Archaea, there is a higher ratio of rRNA introns in the Desulfurococcales and Thermoproteales subbranches in the Crenarchaeota branch. 4) For the three primary phylogenetic groups, the highest ratio of rRNA introns per rRNA gene is for the Eucarya, and for the phylogenetic groups within the Eucarya that have significant numbers of rRNA sequences, the ratio is highest in the fungi. Here, the ratios of rRNA introns per rRNA gene are similar between the nucleus and mitochondria (1.34 for the nucleus, 1.20 for the mitochondria). A significant number of rRNA introns occurs in the plants, with similar ratios of rRNA intron/ rRNA gene for the nucleus, chloroplast, and mitochondria (0.36 for the nucleus, 0.38 for the chloroplast, and 0.34 for the mitochondria). In sharp contrast with the fungi and plants, only one intron has been documented in an animal rRNA, occurring within the Calliphora vicina nuclear-encoded 23S-like rRNA (GenBank accession number K02309).

Each of the two special "Unclassified" rRNA intron groups has a specific phylogenetic bias. Archaeal rRNA introns, which have unique sequence and structural characteristics [83], have not yet been observed within the Euryarchaeota or Korarchaeota; in fact, no non-Archaeal introns have been found in Archaea rRNAs to date. Splicesomal rRNA introns have only been reported in 31 different genera in the Ascomycota [84]. Table 4A also presents the numbers of (complete or nearly so) rRNA sequences in the same phylogenetic groups in order to address the question of sampling bias. Two important caveats to this data must be considered. First, the numbers of rRNA sequences are an underestimate, since many rRNA introns are published with only short flanking exon sequences and do not meet the 90% completeness criterion for inclusion in this rRNA sequence count. The second caveat is that many rRNA sequences contain multiple introns (see Table 3 and related discussion, above, for more information). Of the 51 phylogenetic group/cell location combinations shown in Table 4 that may contain rRNA introns, 15 (29%) have a intron:rRNA sequence ratio greater than 1.0, indicating a bias toward introns within those groups. Introns are comparatively rare within the 26 (51%) groups that have a ratio below 0.3; ten of these 26 groups contain no known rRNA introns. Ten (20%) of the groups have intermediate ratios (between 0.3 and 1.0).

A more detailed phylogenetic distribution is available in Table 4B. The first three fields contain levels 2, 3, and 4 of the NCBI phylogeny, followed by fields for the genus of the organism, cell location, exon (16S or 23S rRNA), and intron type. Each of these classifications include a link to the complete details (organism name, phylogeny, cell location, exon, intron position, intron number, accession number, and structure diagram (when available)) for the intron sequences in that group.