Table 1.
Distribution of cuckoo RNAs. The table summarizes the number of cuckoo RNAs and their distribution across CINs for each species. The occurrences of cuckoo RNAs divided into structural variants are displayed in columns HP2 to HP4 Columns CIN1–CIN6 show the distribution of cuckoo RNAs within the 6 CINs. Each digit represents a cuckoo RNA within a CIN, while the digit's value reflects the number of modules. Unless denoted by a leading character (c = secondary chromosome, p = plasmid) a CIN and therefore the corresponding cuckoo RNA is located on the primary chromosome of the respective bacterium. The first row, for example, reads in words as follows: “In Brucella abortus A13334, we find 4 cuckoo RNAs, one with 2 hairpins, 2 with 3 hairpins, and one with 4 hairpins. The 4HP cuckoo is found on the main chromosome in neighborhood CIN1; in the same neighborhood, but on the secondary chromosome, we find a 2HP cuckoo. The 3HP cuckoos are found on the main chromosome in neighborhood CIN5, and on the secondary chromosome in neighborhood CIN6.” See Table S1 for complete sequences and detailed results.
| Species | HP2 | HP3 | HP4 | CIN1 | CIN2 | CIN3 | CIN4 | CIN5 | CIN6 |
|---|---|---|---|---|---|---|---|---|---|
| Polymorphum gilvum SL003B-26A1 | 0 | 1 | 1 | ||||||
| Brucellaceae | |||||||||
| Brucella abortus A13334 | 1 | 2 | 1 | 4;c2 | 3 | c3 | |||
| Brucella abortus S19 | 1 | 2 | 1 | 4;c2 | 3 | c3 | |||
| Brucella abortus bv. 1 str. 9-941 | 1 | 1 | 1 | 4;c2 | 3 | ||||
| Brucella canis ATCC 23365 | 1 | 1 | 1 | 4 | 3 | c2 | |||
| Brucella canis HSK A52141 | 1 | 1 | 1 | 4 | 3 | c2 | |||
| Brucella melitensis ATCC 23457 | 1 | 1 | 1 | 4;c2 | 3 | ||||
| Brucella melitensis M28 | 1 | 1 | 1 | 4;c2 | 3 | ||||
| Brucella melitensis M5-90 | 1 | 1 | 1 | 4;c2 | 3 | ||||
| Brucella melitensis NI | 1 | 1 | 1 | 4;c2 | 3 | ||||
| Brucella melitensis biovar Abortus 2308 | 2 | 1 | 1 | 4;c2 | 3 | c2 | |||
| Brucella melitensis bv. 1 str. 16M | 2 | 1 | 1 | 4 | 3 | c2 | |||
| Brucella microti CCM 4915 | 2 | 1 | 1 | 4;c2 | 3 | c2 | |||
| Brucella ovis ATCC 25840 | 1 | 1 | 1 | 4;c2 | |||||
| Brucella pinnipedialis B2/94 | 1 | 2 | 1 | 4;c2 | 3 | c3 | |||
| Brucella suis 1330 | 1 | 2 | 1 | 4;c2 | 3 | c3 | |||
| Brucella suis ATCC 23445 | 1 | 2 | 1 | 4;c2 | |||||
| Brucella suis VBI22 | 1 | 2 | 1 | 4;c2 | 3 | c3 | |||
| Ochrobactrum anthropi ATCC 49188 | 0 | 4 | 1 | 4;c3 | |||||
| Hyphomicrobiaceae | |||||||||
| Pelagibacterium halotolerans B2 | 0 | 2 | 0 | ||||||
| Phyllobacteriaceae | |||||||||
| Chelativorans sp. BNC1 | 2 | 4 | 0 | 3 | |||||
| Mesorhizobium australicum WSM2073 | 0 | 5 | 0 | 333 | |||||
| Mesorhizobium ciceri biovar biserrulae WSM1271 | 0 | 6 | 0 | 333 | |||||
| Mesorhizobium loti MAFF303099 | 0 | 6 | 0 | ||||||
| Mesorhizobium opportunistum WSM2075 | 0 | 5 | 0 | 333 | |||||
| Rhizobiaceae | |||||||||
| Agrobacterium tumefaciens str. C58 | 0 | 1 | 2 | ||||||
| Agrobacterium radiobacter K84 | 0 | 3 | 3 | 3 | 3 | 3 | |||
| Agrobacterium sp H13-3 | 0 | 2 | 2 | l4 | |||||
| Agrobacterium vitis S4 | 0 | 3 | 3 | c4 | |||||
| Rhizobium etli CFN 42 | 0 | 4 | 2 | p4 | 3 | 3 | |||
| Rhizobium etli CIAT 652 | 1 | 3 | 3 | p4 | 3 | ||||
| Rhizobium etli bv. mimosae str. Mim1 | 0 | 4 | 1 | p4 | 3 | 3 | |||
| Rhizobium leguminosarum bv. trifolii WSM1325 | 0 | 4 | 4 | 3;p4;p4 | 3 | 3 | |||
| Rhizobium leguminosarum bv. trifolii WSM2304 | 1 | 4 | 2 | 3;p4 | 3 | 3 | |||
| Rhizobium leguminosarum bv. viciae 3841 | 0 | 4 | 1 | p4 | 3 | ||||
| Rhizobium tropici CIAT 899 | 0 | 3 | 1 | p4 | 3 | 3 | |||
| Sinorhizobium fredii HH103 | 0 | 6 | 0 | 33 | p3 | ||||
| Sinorhizobium fredii NGR234 | 0 | 4 | 0 | 33 | p3 | ||||
| Sinorhizobium fredii USDA 257 | 0 | 6 | 0 | 33 | 3 | ||||
| Sinorhizobium medicae WSM419 | 1 | 4 | 2 | 33;p4 | p3 | ||||
| Sinorhizobium meliloti 1021 | 0 | 5 | 1 | ||||||
| Sinorhizobium meliloti 2011 | 0 | 5 | 1 | 3 | p3 | ||||
| Sinorhizobium meliloti AK83 | 0 | 5 | 1 | 3 | 3 | c3 | |||
| Sinorhizobium meliloti BL225C | 0 | 4 | 1 | 33 | 3 | p3 | |||
| Sinorhizobium meliloti GR4 | 0 | 4 | 1 | 33 | 3 | p3 | |||
| Sinorhizobium meliloti Rm41 | 0 | 5 | 1 | 3 | p3 | ||||
| Sinorhizobium meliloti SM11 | 0 | 4 | 1 | 33 | 3 | p3 | |||
| Rhodobacteraceae | |||||||||
| Parvibaculum lavamentivorans DS-1 | 1 | 0 | 0 | ||||||
| Dinoroseobacter shibae DFL 12 | 1 | 0 | 0 | ||||||
| Jannaschia sp. CCS1 | 3 | 0 | 0 | 222 | |||||
| Ketogulonicigenium vulgare WSH-001 | 0 | 1 | 0 | ||||||
| Ketogulonicigenium vulgare Y25 | 0 | 1 | 0 | ||||||
| Loktanella vestfoldensis DSM 16212 | 2 | 1 | 0 | ||||||
| Loktanella vestfoldensis SKA53 | 2 | 1 | 0 | 223 | |||||
| Oceanicola batsensis HTCC2597 | 2 | 0 | 1 | 24 | |||||
| Oceanicola granulosus HTCC2516 | 4 | 1 | 0 | 22223 | |||||
| Octadecabacter antarcticus 307 | 2 | 0 | 4 | ||||||
| Octadecabacter arcticus 238 | 3 | 1 | 3 | ||||||
| Paracoccus aminophilus JCM 7686 | 0 | 0 | 2 | 44 | |||||
| Paracoccus denitrificans PD1222 | 4 | 0 | 1 | 22224 | |||||
| Phaeobacter gallaeciensis 2.10 | 2 | 0 | 0 | 22 | |||||
| Phaeobacter gallaeciensis DSM 17395 | 2 | 0 | 0 | 22 | |||||
| Phaeobacter gallaeciensis DSM 26640 | 2 | 0 | 0 | ||||||
| Pseudovibrio sp FO-BEG1 | 0 | 0 | 1 | ||||||
| Rhodobacter capsulatus SB 1003 | 4 | 0 | 0 | 2222 | |||||
| Rhodobacter sphaeroides 2.4.1 | 7 | 0 | 0 | 2222222 | |||||
| Rhodobacter sphaeroides ATCC 17025 | 4 | 0 | 0 | 2222 | |||||
| Rhodobacter sphaeroides ATCC 17029 | 9 | 0 | 0 | 222222222 | |||||
| Rhodobacter sphaeroides KD131 | 7 | 0 | 0 | 2222222 | |||||
| Roseobacter denitrificans OCh 114 | 2 | 0 | 0 | 22 | |||||
| Roseobacter litoralis OCh 149 | 2 | 0 | 0 | 22 | |||||
| Roseovarius nubinhibens ISM | 2 | 0 | 0 | 2 | |||||
| Roseovarius sp. 217 | 2 | 0 | 0 | 22 | |||||
| Ruegeria pomeroyi DSS-3 | 3 | 0 | 0 | 222 | |||||
| Ruegeria sp TM1040 | 2 | 0 | 0 | 22 | |||||
| Sagittula stellata E-37 | 3 | 1 | 0 | 2223 | |||||
| Sulfitobacter sp. EE-36 | 1 | 0 | 1 | 24 | |||||
| Sulfitobacter sp NAS-14.1 | 2 | 0 | 1 | 24 |