Table 1.
Summary of 39 identified archaeal group I introns showing the name we use to refer to each intron; GenBank accession; phylum assignment (R: inferred by RDPClassifier; G: annotated in GenBank; –: unclassified by either); coordinates of the intron in the source sequence; E-value of the most significant Infernal hit to this intron; insertion position in the host ribosomal RNA gene in canonical E. coli coordinate numbering (32); and citation for the source sequence. For four phylum assignments, noted by ?, Genbank annotation and RDPClassifier inference were in conflict, and we chose one (see Materials and Methods). For 14 assignments, noted by *, an SSU rRNA was present but RDPClassifier was unable to resolve a phylum-level assignment. IB4.16 is intentionally missing (see text). An expanded table is provided as a parseable .csv file in supplementary data.
| Intron | Sequence | Intron | Infernal | Insertion | ||
|---|---|---|---|---|---|---|
| Name | Accession | Phylum | Coordinates | E-value | Position | Reference |
| IA3.1 | CP010426.1 | Woesearchaeota (R) | 664815–664111 | 2.2e–16 | LSU/2593 | (33) |
| IA3.2 | LQMQ01000054.1 | Euryarchaeota* (G) | 4017–4815 | 4.6e–8 | LSU/2500 | (34) |
| IA3.3 | LQMP01000030.1 | Euryarchaeota (G+R) | 66091–65273 | 3.3e–11 | LSU/2500 | (34) |
| IA3.4 | JWKY01000014.1 | – | 16576–15805 | 4.4e–12 | LSU/2593 | (33) |
| IA3.5 | ASMP01000002.1 | Pacearchaeota (R) |
130592–130914 | 7.0e–33 | LSU/2593 | (35) |
| IA3.6 | KP308561.1 | Pacearchaeota (R) | 16134–15526 | 2.9e–27 | LSU/2593 | (33) |
| IA3.7 | KP308720.1 | –* | 23163–23468 | 3.5e–42 | LSU/2593 | (33) |
| IA3.8 | KY476711.1 | –* | 66905–66301 | 1.1e–26 | LSU/2593 | (36) |
| IA3.9 | MNVE01000016.1 | Micrarchaeota* (G) | 260342–261072 | 2.2e–15 | LSU/2593 | (37) |
| IA3.10 | MNVF01000017.1 | Micrarchaeota (G) | 6638–7348 | 4.9e–16 | LSU/2593 | (37) |
| IA3.11 | MNVH01000001.1 | Micrarchaeota* (G) | 9089–8693 | 1.6e–36 | LSU/2593 | (37) |
| IA3.12 | MNVZ01000017.1 | Pacearchaeota (G) | 14519–14202 | 2.8e–30 | LSU/2593 | (37) |
| IB4.1 | CBTY010000008.1 | Thaumarchaeota (G+R) | 399334–399054 | 1.0e–34 | LSU/1931 | (38) |
| IB4.2 | KP308713.1 | Woesearchaeota (R) | 1026–667 | 2.3e–32 | LSU/1931 | (33) |
| IB4.3 | KP308715.1 | Woesearchaeota (R) | 33361–33696 | 8.1e–39 | LSU/1931 | (33) |
| IB4.4 | KP308717.1 | Woesearchaeota (R) | 8526–8928 | 3.0e–32 | LSU/1931 | (33) |
| IB4.5 | KP308748.1 | Woesearchaeota (R) | 21438–21748 | 1.4e–25 | LSU/1931 | (33) |
| IB4.6 | KP308561.1 | Pacearchaeota (R) | 17157–16694 | 9.1e–31 | LSU/1931 | (33) |
| IB4.7 | KP308720.1 | –* | 21440–21763 | 1.4e–35 | LSU/1923 | (33) |
| IB4.8 | AEIX01000219.1 | Nanohaloarchaeota (G+R) | 2242–1950 | 7.8e–21 | SSU/1498 | (39) |
| IB4.9 | BA000048.1 | Aigarchaeota (G) |
1314432–1313300 | 2.0e–7 | LSU/1923 | (40) |
| IB4.10 | AEIX01000215.1 | Nanohaloarchaeota (G) | 10957–11697 | 4.5e–10 | LSU/1931 | (39) |
| IB4.11 | AP011903.1 | Thaumarchaeota (R) |
23185–23940 | 1.0e–6 | LSU/1923 | (40) |
| IB4.12 | AQRL01000028.1 | Woesearchaeota (R) |
30565–31289 | 9.2e–17 | LSU/1931 | (35) |
| IB4.13 | ASPK01000003.1 | Thaumarchaeota* (G) | 12290–11538 | 7.5e–5 | LSU/1923 | (35) |
| IB4.14 | AGCY01000458.1 | Euryarchaeota (G+R) | 2850–3533 | 1.1e–11 | LSU/1931 | (41) |
| IB4.15 | KP308720.1 | –* | 21772–22514 | 3.3e–15 | LSU/1931 | (33) |
| IB4.17 | MNVF01000017.1 | Micrarchaeota (G) | 5465–5748 | 2.4e–29 | LSU/1923 | (37) |
| IB4.18 | MNVH01000001.1 | Micrarchaeota* (G) | 10442–9750 | 6.2e–8 | LSU/1923 | (37) |
| IB4.19 | MNVH01000001.1 | Micrarchaeota* (G) | 13564–12830 | 2.7e–16 | SSU/1498 | (37) |
| IB4.20 | MFRR01000014.1 | Micrarchaeota (G) | 65096–64410 | 5.0e–11 | LSU/1923 | (42) |
| IB4.21 | MNVZ01000017.1 | Pacearchaeota (G) | 15452–15175 | 3.0e–27 | LSU/1923 | (37) |
| IB4.22 | MFWP01000012.1 | Pacearchaeota* (G) | 2846–3187 | 5.2e–28 | LSU/1931 | (42) |
| IB4.23 | MNFA01000040.1 | Thaumarchaeota (G+R) | 5119–5802 | 1.9e–10 | LSU/1931 | (43) |
| IB4.24 | MNVG01000014.1 | Micrarchaeota* (G) | 9943–10190 | 1.7e–29 | LSU/1931 | (37) |
| IB4.25 | MNVJ01000003.1 | Micrarchaeota* (G) | 25302–24603 | 6e–14 | LSU/1931 | (37) |
| IB4.26 | MNVJ01000003.1 | Micrarchaeota* (G) | 28477–27735 | 4.3e–17 | SSU/1498 | (37) |
| IB4.27 | MNWW01000056.1 | Woesearchaeota (G+R) | 8341–9021 | 1.3e–10 | LSU/1931 | (37) |
| IB4.28 | NJDR01000009.1 | Aenigmarchaeota (G) | 12303–13059 | 3.5e–10 | LSU/1923 | (44) |