Skip to main content

Table 2 Codon usage in highly and weakly expressed genes

From: A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

   Spiro hi1 Spiro weak2 Giardia hi3 Giardia weak4    Spiro hi1 Spiro weak2 Giardia hi3 Giardia weak4
   # RSCU5 # RSCU5 # RSCU5 # RSCU    # RSCU5 # RSCU5 # RSCU5 # RSCU5
Phe UUU 80 0.62 3520 1.21 51 0.41 3584 0.99 Ser UCU 208 3.11 2235 1.51 75 1.20 3962 1.53
  UUC 180 1.38 2317 0.79 197 1.59 3689 1.01   UCC 114 1.71 1009 0.68 125 2.01 2559 0.99
Leu UUA 62 0.77 3475 1.84 4 0.05 1394 0.44   UCA 38 0.57 2035 1.38 22 0.35 2218 0.86
  UUG 17 0.21 1639 0.87 27 0.32 2466 0.77   UCG 7 0.10 1027 0.69 77 1.24 1825 0.70
  CUU 184 2.30 2163 1.15 123 1.44 5060 1.59 Pro CCU 142 2.27 1372 1.31 49 0.65 2177 1.05
  CUC 210 2.62 1470 0.78 239 2.80 4307 1.35   CCC 87 1.39 650 0.62 118 1.56 2010 0.97
  CUA 0 0.00 1220 0.65 15 0.18 2302 0.72   CCA 20 0.32 1570 1.50 41 0.54 2369 1.14
  CUG 7 0.09 1366 0.72 105 1.23 3601 1.13   CCG 1 0.02 608 0.58 94 1.25 1720 0.83
Ile AUU 155 0.96 4600 1.52 92 0.62 4220 1.09 Thr ACU 194 1.90 2206 1.36 45 0.53 2757 0.97
  AUC 302 1.87 1977 0.66 302 2.05 4272 1.11   ACC 170 1.66 1322 0.81 103 1.22 2811 0.98
  AUA 28 0.17 2476 0.82 48 0.33 3086 0.80   ACA 34 0.33 1929 1.19 57 0.68 3544 1.24
Met AUG 164 1.00 2280 1.00 181 1.00 4180 1.00   ACG 11 0.11 1047 0.64 132 1.57 2306 0.81
Val GUU 261 2.09 2782 1.61 98 0.77 3608 1.27 Ala GCU 321 2.48 2448 1.27 118 0.82 3529 1.00
  GUC 140 1.12 1252 0.72 297 2.32 3375 1.18   GCC 143 1.11 1570 0.82 228 1.59 3738 1.06
  GUA 81 0.65 1668 0.97 27 0.21 1591 0.56   GCA 46 0.36 2233 1.16 96 0.67 4588 1.30
  GUG 18 0.14 1210 0.70 90 0.70 2819 0.99   GCG 7 0.05 1437 0.75 132 0.92 2310 0.65
Tyr UAU 145 1.34 2703 1.31 59 0.55 3095 1.00 Cys UGU 45 0.58 1943 0.80 28 0.39 1437 0.80
  UAC 71 0.66 1430 0.69 156 1.45 3110 1.00   UGC 110 1.42 2893 1.20 116 1.61 2137 1.20
Gln/TER 6 UAA 58 0.83 3576 1.67 21 1.91 54 0.94 TER UGA 30 1.00 140 1.00 6 0.55 62 1.08
  UAG 44 0.63 1697 0.79 6 0.55 56 0.98 Trp UGG 50 1.00 752 1.00 57 1.00 1458 1.00
His CAU 70 0.85 1239 1.22 17 0.22 1595 0.85 Arg CGU 235 3.37 764 0.99 100 1.18 1661 1.04
  CAC 95 1.15 796 0.78 136 1.78 2151 1.15   CGC 30 0.43 781 1.02 253 2.98 2403 1.51
Gln CAA 30 0.43 1500 0.70 25 0.23 2676 0.73   CGA 1 0.01 392 0.51 19 0.22 1115 0.70
  CAG 147 2.11 1791 0.84 192 1.77 4640 1.27   CGG 1 0.01 352 0.46 7 0.08 1324 0.83
Asn AAU 106 0.68 4502 1.28 61 0.43 3571 0.91 Ser AGU 10 0.15 1269 0.86 15 0.24 1818 0.70
  AAC 208 1.32 2544 0.72 226 1.57 4291 1.09   AGC 24 0.36 1296 0.88 60 0.96 3171 1.22
Lys AAA 191 0.59 5117 1.28 50 0.16 2778 0.53 Arg AGA 141 2.02 1694 2.20 39 0.46 1575 0.99
  AAG 458 1.41 2902 0.72 565 1.84 7623 1.47   AGG 11 0.16 628 0.82 91 1.07 1459 0.92
Asp GAU 208 1.28 3993 1.26 100 0.55 5063 0.97 Gly GGU 345 3.03 2029 1.24 88 0.73 1923 0.79
  GAC 116 0.72 2333 0.74 264 1.45 5424 1.03   GGC 71 0.62 1672 1.02 215 1.77 2699 1.11
Glu GAA 325 1.53 4444 1.24 53 0.24 4072 0.71   GGA 35 0.31 1816 1.11 59 0.49 2797 1.15
  GAG 101 0.47 2716 0.76 389 1.76 7431 1.29   GGG 4 0.04 1029 0.63 123 1.01 2342 0.96
  1. 1)S. salmonicida genes represented by more than 10 ESTs (35 genes, 6948 codons)
  2. 2)S. salmonicida genes unrepresented among the ESTs (682 genes, 122846 codons)
  3. 3)G. lamblia homologs to S. salmonicida genes represented by more than 10 ESTs (33 genes, 7004 codons)
  4. 4)G. lamblia homologs to S. salmonicida genes unrepresented among the ESTs (172 genes, 184988 codons)
  5. 5)Relative synonymous codon usage; the most and least abundant codons for each amino acid are indicated with boldface and italic font, respectively.
  6. 6)UAA and UAG encode glutamine in Spironucleus, and are termination codons in Giardia [25, 26].