From: Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
COG functional categories | Code | OI (n = 40) | FHA (n = 85) | HD (n = 125) | FL (n = 192) | HD vs. FL |
---|---|---|---|---|---|---|
(a) Gene count Mean +/- s.d. | Â | Â | Â | Â | Â | p-value* |
   Chromatine structure and dynamics | B | 0.28 ± 0.45 | 0.44 ± 1.07 | 0.38 ± 0.92 | 1.16 ± 1.28 | 0.4982 |
   Replication, recombination and repair | L | 56.78 ± 26.49 | 161.58 ± 171.99 | 128.04 ± 150.56 | 141.23 ± 55.84 | 0.3035 |
   Transcription | K | 23.70 ± 10.23 | 105.65 ± 74.89 | 79.42 ± 72.84 | 163.82 ± 99.52 | 0.0000 |
   RNA processing and modification | A | 0.70 ± 1.26 | 1.20 ± 2.09 | 1.04 ± 1.87 | 1.11 ± 1.87 | 0.9290 |
   Translation, ribosomal structure and biogenesis | J | 116.68 ± 13.97 | 143.42 ± 25.75 | 134.86 ± 25.83 | 157.62 ± 19.27 | 0.0000 |
   Posttranslational modification, protein turnover, chaperones | O | 39.08 ± 10.84 | 74.60 ± 41.27 | 63.23 ± 38.31 | 94.13 ± 39.75 | 0.0000 |
   Intracellular trafficking, secretion, and vesicular transport | U | 29.68 ± 10.05 | 59.62 ± 44.82 | 50.04 ± 39.86 | 63.77 ± 44.54 | 0.0002 |
   Signal transduction mechanisms | T | 10.48 ± 8.45 | 56.65 ± 41.04 | 41.87 ± 40.39 | 103.67 ± 67.24 | 0.0001 |
   Cell cycle control, cell division, chromosome partitioning | D | 11.20 ± 5.52 | 21.96 ± 9.96 | 18.52 ± 10.11 | 25.72 ± 7.73 | 0.0000 |
   Defense mechanisms | V | 2.60 ± 4.32 | 20.56 ± 13.81 | 14.82 ± 14.35 | 29.46 ± 14.94 | 0.0000 |
   Cell wall/membrane/envelope biogenesis | M | 39.10 ± 22.84 | 110.27 ± 65.03 | 87.50 ± 64.34 | 130.06 ± 59.91 | 0.0000 |
   Cell motility | N | 8.23 ± 10.53 | 44.73 ± 44.12 | 33.05 ± 40.57 | 53.24 ± 51.60 | 0.0172 |
   Cytoskeleton | Z | 0.08 ± 0.47 | 0.28 ± 1.09 | 0.22 ± 0.94 | 0.24 ± 0.78 | 0.8927 |
   Nucleotide transport and metabolism | F | 26.70 ± 10.47 | 54.55 ± 19.22 | 45.64 ± 21.33 | 69.52 ± 15.52 | 0.0000 |
   Amino acid transport and metabolism | E | 39.65 ± 20.39 | 152.06 ± 108.15 | 116.09 ± 104.05 | 213.71 ± 106.02 | 0.0000 |
   Carbohydrate transport and metabolism | G | 24.05 ± 10.89 | 112.52 ± 86.46 | 84.21 ± 82.57 | 132.33 ± 70.07 | 0.0000 |
   Lipid transport and metabolism | I | 26.15 ± 11.18 | 58.54 ± 45.94 | 48.18 ± 41.22 | 81.96 ± 54.49 | 0.0000 |
   Coenzyme transport and metabolism | H | 40.25 ± 17.78 | 82.91 ± 47.76 | 69.26 ± 45.21 | 109.84 ± 39.55 | 0.0000 |
   Inorganic ion transport and metabolism | P | 22.48 ± 7.80 | 89.40 ± 61.77 | 67.98 ± 59.89 | 127.67 ± 60.67 | 0.0000 |
   Secondary metabolites biosynthesis, transport and catabolism | Q | 6.18 ± 6.09 | 32.34 ± 40.30 | 23.97 ± 35.52 | 50.04 ± 44.50 | 0.0000 |
   Energy production and conversion | C | 48.63 ± 16.77 | 111.98 ± 75.61 | 91.70 ± 69.58 | 148.99 ± 82.31 | 0.0000 |
   General function prediction only | R | 53.58 ± 27.82 | 187.75 ± 106.15 | 144.82 ± 108.75 | 265.65 ± 119.15 | 0.0000 |
   Function unknown | S | 43.23 ± 27.19 | 184.84 ± 124.19 | 139.52 ± 122.80 | 262.59 ± 118.90 | 0.0000 |
Total | Â | 669.43 | 1867.85 | 1484.35 | 2427.53 | Â |
(b) Percent of genes in the different functional categories (%) | ||||||
Information storage and processing (B+L+K+A+J) | Â | 29.60 | 22.07 | 23.16 | 19.15 | Â |
Cellular processes and signalling (O+U+T+D+V+M+N+Z) | Â | 20.98 | 20.81 | 20.83 | 20.61 | Â |
Metabolism (F+E+G+I+H+P+Q+C) | Â | 34.97 | 37.17 | 36.85 | 38.48 | Â |
Poorly characterized (R+S) | Â | 14.46 | 19.95 | 19.16 | 21.76 | Â |