TABLE 1.
Ribosomal genes missing in organisms with tiny genomesa
| Organism nameb | Genome size (kb) | Taxonomy | Missing and highly diverged protein(s) (n)c | Protein(s) found byTBLASTn |
|---|---|---|---|---|
| Bacteria | ||||
| “Ca. Nasuia deltocephalinicola NAS-ALF” | 112.1 | Betaproteobacteria | L1, L9, L10, L13, L18, L19, L21, L22, L24, L28, L29, L30, L31, L32, L33, L35, S16, S18, S20, S21 (11) | |
| “Ca. Vidania fulgoroideae OLIH” | 136.1 | Betaproteobacteria | L9, L10, L17, L19, L21, L22, L23, L24, L28, L29, L30, L31, L32, L35, S2, S6, S15, S16, S17, S20, S21 (11) | |
| “Ca. Hodgkinia cicadicola Dsem” | 143.8 | Alphaproteobacteria | L1, L9, L19, L23, L24, L29, L30, L31, L32, L34, S15, S20, S21 (11) | S6 |
| “Ca. Tremblaya phenacola PAVE” | 171.5 | Betaproteobacteria | L9, L21, L23, L24, L29, L32, L34 (6) | |
| “Ca. Carsonella ruddii DC” | 174.0 | Gammaproteobacteria | L9, L10, L17, L18, L19, L21, L23, L24, L25, L29, L30, L32, L34, L35, S6, S15, S18, S20, S21 (16) | |
| “Ca. Sulcia muelleri PUNC” | 190.7 | Bacteroidetes | L23, L24, L29, L30 (4) | |
| “Ca. Zinderia insecticola CARI” | 208.6 | Betaproteobacteria | L9, L23, L28, L29, L30, L35, S6, S18, S20 (4) | |
| “Ca. Uzinura diaspidicola ASNER” | 263.4 | Bacteroidetes | L29 | |
| “Ca. Walczuchella monophlebidarum” | 309.3 | Bacteroidetes | L29 | |
| “Ca. Mikella endobia” | 352.8 | Gammaproteobacteria | — | |
| “Ca. Portiera aleyrodidarum” | 357.5 | Gammaproteobacteria | L30 | |
| “Ca. Evansia_muelleri” | 357.5 | Gammaproteobacteria | L9, L30 | |
| “Ca. Profftella armatura DC” | 464.9 | Betaproteobacteria | — | |
| “Ca. Purcelliella pentastirinorum” | 479.9 | Gammaproteobacteria | — | |
| “Ca. Moranella endobia” | 538.2 | Gammaproteobacteria | — | |
| Mycoplasma genitalium G37b | 580.1 | Mollicutes | L25, L30, S1 | |
| “Ca. Riesia pediculicola” | 582.1 | Gammaproteobacteria | L30 | |
| Bacterium AB1 | 593.4 | N/A | L9, L10, L19, L21, L23, L25, L29, L30, L31, L32, L33, L35, S6, S15, S18, S20, S21 (15) | L34 |
| Cand. division Kazan bacterium GW2011_GWA1_50_15 | 602.6 | Other bacteria | L30, S21 | L34 |
| Blattabacterium sp. (Blattella germanica) strain Bge | 641.0 | Bacteroidetes | L30 | |
| Buchnera aphidicola APS (Acyrthosiphon pisum) | 655.7 | Gammaproteobacteria | — | |
| “Ca. Hepatoplasma crinochetorum Av”b | 657.1 | Mollicutes | L9, L25, L30, S1, S21 | |
| “Ca. Nanosynbacter lyticus TM7x” | 705.1 | Other bacteria | L9, L25, L30, L32 | |
| “Ca. Campbellbacteria bacterium GW2011 OD1 34 28” | 752.6 | Other bacteria | L1, L29, L30 | L36 |
| “Ca. Blochmannia pennsylvanicus BPEN” | 791.7 | Gammaproteobacteria | L30 | |
| “Ca. Woesebacteria bacterium GW2011 GWF1_31_35” | 819.5 | Other bacteria | L9, L29, L30 | |
| “Ca. Fokinia solitaria” | 837.3 | Alphaproteobacteria | L30 | |
| Cand. division TM6 bacterium GW2011 GWF2_28_16 | 853.1 | Other bacteria | L9, L30, L32, S21 | L36 |
| Neorickettsia sennetsu Miyayama | 859.0 | Alphaproteobacteria | L30 | |
| Cand. division WWE3 bacterium RAAC2_WWE3_1 | 878.1 | Other bacteria | L9, L30, L32 | L34, L36, S14 |
| Berkelbacteria bacterium GW2011 GWE1_39_12 | 915.1 | Other bacteria | L30 | L36 |
| “Ca. Xiphinematobacter Idaho Grape” | 915.9 | Verrucomicrobia | — | |
| Tropheryma whipplei Twist | 927.3 | Actinobacteria | S21 | |
| “Ca. Wolfebacteria bacterium GW2011_GWB1_47_1” | 984.4 | Other bacteria | L1, L30, L33, S21 | L32, L34 |
| Archaead | ||||
| Nanoarchaeum equitans Kin4-M | 490.9 | Other archaea | L13e, L40e, S25e, S30 | L24e, L37e |
| “Ca. Nanopusillus acidilobi” | 605.9 | Other archaea | L13e, L29, L39e, S27e, S30 | L6/L9e, L16/L10ae, L15e, L22, L24, L35ae, L37e, S6e, S15/S13e |
| “Ca. Mancarchaeum acidiphilum Mia14” | 952.3 | Other archaea | L13e, L20a/L18a, L35ae, L37e, S17e, S25e, S27e, S30 | |
| Nanohaloarchaea archaeon SG9 | 1,118.6 | Euryarchaeota | L13e, L14e, L20a/L18a, L30e, L31e, L34e, L35ae, L39e, S30 | L18, L24e, L40e, S2, S28e |
| Archaeon GW2011_AR15 | 1.157.8 | Other archaea | L13e, L20a/L18a, L40e, S25e, S26e, S30 |
Organism names, genome sizes, and taxonomic assignments are taken from the NCBI Taxonomy database (81) and are listed as in the COG database (30). The organisms are listed in the order of their genome sizes. Cand., candidate; Ca., Candidatus; N/A, not available.
For genome sizes over 600 kb, only selected organisms are shown. Only two representatives of Tenericutes (Mollicutes) are included. See text for discussion.
Ribosomal proteins that are missing in several distinct lineages are shown in bold; highly diverged proteins and fragments not recognized by the standard CD-search (82) are in italics. A dash indicates the presence of the full set of RPs.
No complete archaeal genomes sequenced so far encode L9, L7/L12, L17, L19, L20, L21, L25, L27, L28, L31 to L36, S1, S6, S16, S18, S20, and S21 (see Table S1). The proteins listed here are those present in other, larger archaeal genomes.