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Table 2 Comparison of candidate markers for interspecies phylotyping in Nannochloropsis genus

From: Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae

Gene Origin Size Difference*% Euclidean distance*** SD****
Interspecies Intraspecies**
rps14_mt mt 297 37.71 0.34 0.397 0.046
ycf34 pt 252-261 33.72 0.00 0.409 0.038
rps14_mt-atp9 mt 102-195 32.83 0.00 0.500 0.048
rps4_mt mt 726 32.09 0.41 0.260 0.031
rpl6_mt mt 552 32.07 0.36 0.263 0.036
ycf34-psbD pt 204-224 31.72 0.13 0.211 0.018
rpl5_mt mt 525-540 31.67 0.57 0.299 0.037
clpA pt 447-450 29.33 0.22 0.328 0.040
orf53 mt 156-162 29.01 0.00 0.258 0.041
rpl14_mt mt 381 28.35 0.79 0.167 0.023
trnQ(uug)-groEL pt 269-274 28.00 0.00 0.253 0.032
trnL(uag)-trnW(cca) pt 648-673 27.99 0.46 0.234 0.021
ITS2 nc 385-499 27.67 0.52 - -
rps2-rpoC2 pt 162-193 25.63 1.04 0.281 0.036
rpl16_mt mt 432 24.54 0.00 0.098 0.018
nad4 mt 1578 23.76 0.63 0.038 0.008
atp9-rps13_mt mt 215-233 23.50 0.43 0.107 0.022
ccs1 pt 1260-1272 22.90 0.00 0.111 0.010
rpl1 pt 687 22.56 0.00 0.114 0.012
ilvB pt 1479 21.37 0.00 0.084 0.008
rpl6 pt 543 20.99 0.18 0.054 0.008
ccsA pt 918-921 20.96 0.22 0.105 0.015
chlN pt 1326-1335 20.37 0.00 0.062 0.008
ycf59 pt 1044 20.31 0.00 0.054 0.007
cbbX pt 1011 19.88 0.10 0.053 0.008
chlL pt 867 19.26 0.12 0.026 0.005
rps4 pt 627 19.14 0.00 0.029 0.005
rpoB pt 3168 19.10 0.03 0.034 0.004
dnaK pt 1809 19.02 0.11 0.030 0.004
clpC-II pt 1155 18.87 0.09 0.020 0.004
atp8-orf228 mt 1294-1413 18.55 0.29 0.140 0.012
chlB pt 1521-1524 18.37 0.00 0.023 0.005
ThiS-rbcL pt 314-330 18.15 0.00 0.052 0.011
nad3 mt 369 17.89 0.27 0.108 0.009
ycf36-petN pt 391-397 17.84 0.00 0.055 0.010
rps16 pt 255 17.65 0.00 0.119 0.025
cox1 mt 1521 17.55 0.13 0.144 0.018
ycf49 pt 294-297 16.84 0.00 0.035 0.007
ycf3 pt 504 16.47 0.00 0.059 0.009
rpl23 pt 360 16.11 0.00 0.062 0.007
cob mt 1161 15.25 0.00 0.207 0.024
ilvB-rpl35 pt 504-512 15.04 0.00 0.091 0.019
nad2 mt 1482 14.71 0.34 0.039 0.005
hyp.protein pt 645-699 14.57 0.14 0.086 0.009
rps13 pt 372 14.25 0.00 0.107 0.011
cox3 mt 813 13.65 0.12 0.221 0.021
cox2 mt 909 13.53 0.00 0.215 0.018
tufA pt 1230-1275 13.36 0.08 0.067 0.009
rps7 pt 456-477 12.55 0.00 0.160 0.017
atpG pt 477-483 11.18 0.00 0.171 0.014
rbcL pt 1464 10.04 0.00 0.213 0.021
psaE pt 204 9.80 0.00 0.199 0.017
rrn23_mt mt 2235 8.18 0.18 0.365 0.038
rrn16_mt mt 1491-1494 6.87 0.00 0.381 0.035
psbA pt 1083 4.16 0.00 0.364 0.036
18S nc 1790-1792 2.51 0.16 - -
  1. Note: “-” indicated that the gene was not encoded by the organelle genomes. *Difference = SNP/Size; **Difference between IMET1 and CCMP531; ***A measure of the similarity between two trees calculated from the two p-distance matrixes that each represents a phylogenetic tree; ****Square deviation of the corresponding p-distance between two matrixes.