Table 2.
Top 10 arCOGs with Short Branches
| Top 10 arCOGs with Short Branches | |||
|---|---|---|---|
| arCOG, Protein, Annotation | Clade with Short and/or Long Branches (rank)a | Commentsb | |
| 1 | arCOG01171, KaiC, KaiC-superfamily ATPase implicated in signal transduction | ↓(1) Thermococci; | Large family with multiple paralogs (McRobbie etal. 2009). Likely diversification of the family through sub- and neofunctionalization, with acceleration and deceleration of the evolution of the different copies. |
| ↑(35) Methanocellales; | |||
| ↓(57) Archeaoglobi | |||
| 2 | arCOG02391, CheY, Rec domain | ↓(4) Methanomicrobiales; | Large family with multiple paralogs. The short branches in Methanomicrobiales clade correspond to an ancestral variant, located in a conserved neighborhood of genes involved in chemotaxis. |
| ↑(34) Methanocellales | |||
| 3 | arCOG04272, CobT, NaMN: DMB | ↓(5) Thermococci | Likely xenologous gene displacement via HGT from Crenarchaea to Thermococci. Possible neofunctionalization. |
| 4 | arCOG01568, MscS, Small-conductance mechanosensitive channel | ↓(7) Archaeoglobi | Likely multiple HGT events between archaea and bacteria. Potential coevolution with uncharacterized protein of arCOG01766 family. Possible subfunctionalization. |
| 5 | arCOG01057, HxlR, DNA-binding transcriptional regulator, HxlR family | ↓(8) Methanomicrobiales | Probable HGT from bacteria to Methanomicrobiales+ Methanosarcinales. Encoded in a predicted operon with hydroxylamine reductase (arCOG02430).Likely subfunctionalization by recruitment as a transcriptional regulator for hydroxylamine reductase. |
| 6 | arCOG01715, SufB, Cysteine desulfurase activator SufB | ↓(9) Thaumarchaeota; | Duplication in the common ancestor of Thaumarchaeota and Crenarchaeota. Subfunctionalization of the two paralogs is likely given considerable sequence divergence (Iwasaki 2010). |
| ↑(44) Sulfolobi | |||
| 7 | arCOG01107, ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase or related deacylase | ↓(10) Thermococcales | Large family with multiple paralogs many apparent cases of HGT. Metal-binding site conserved in all enzymes (Bienvenue etal. 2003) with minor divergences. Subfunctionalization could be related to a tight functional link with SAM-dependent methyltransferase protein (arCOG00111) present in the predicted operon. |
| 8 | arCOG02267, PitA, Phosphate/sulphate permease | ↓(11) Archaeoglobi | Two paralogs in most of Archaeoglobi. Likely coevolves with PhoU-like protein (arCOG02640) involved in regulation of phosphate transport. Possible subfunctionalization accompanied by stronger purifying selection. |
| 9 | arCOG04308, -, Uncharacterized protein | ↓(12) Sulfolobi; | No paralogs, archaea-specific. In a conserved neighborhood with an uncharacterized Zn-finger containing protein (arCOG00578). No new function predicted, the cause behind strong purifying selection is not clear. |
| ↓(60) Methanocellales | |||
| 10 | arCOG04243, RplS, Ribosomal protein S9 | ↓(13) Thermococci | No paralogs, archaea-specific. No new function predicted, the cause behind strong purifying selection is not clear. |
a
Upward arrow shows an exceptionally long branch and downward arrow shows an exceptionally short branch.
b
For additional information, see ftp://ftp.ncbi.nlm.nih.gov/pub/wolf/_suppl/archdev.