Table 3. Comparison of topology between the concatenated tree and single trees.
| CDS product | Homolog to: (locus_tag of C. neoformans) | Based on nucleotide sequences | ||||||||||||||||
| Positions used | Highest log likelihood | Bootstrap value of each node*1 | # nodes contained in concatenated tree*2 | Divergence within Trichosporonales*3 | ||||||||||||||
| a | b | c | d | e | f | g | h | i | j | k | l | m | ||||||
| phosphatidylinositol 3-kinase TOR1 | CNF03740 | 7167 | -71807.7691 | 100 | 100 | 100 | (57) | 96 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 12/13 | 0.2765973 |
| glutamate synthase (NADH) | CNJ02910 | 6525 | -58590.6785 | 100 | 100 | - | 100 | 100 | 100 | 75 | 100 | 100 | 93 | 95 | 100 | 96 | 12/13 | 0.2325986 |
| malate synthase | CNH02910 | 1641 | -13875.1721 | 100 | 100 | 100 | - | (53) | 100 | 100 | 72 | 100 | 100 | 84 | 100 | 90 | 11/13 | 0.2328670 |
| phosphoenolpyruvate carboxykinase | CNI03590 | 1668 | -10299.0077 | 100 | 100 | 81 | 100 | 81 | 75 | 92 | - | 76 | 99 | - | 100 | 97 | 11/13 | 0.1416784 |
| ATP-binding cassette (ABC) transporter | CND00300 | 1932 | -14912.2764 | 100 | 100 | 100 | 81 | - | 100 | 91 | (38) | 100 | 100 | - | 100 | 98 | 10/13 | 0.1990241 |
| glycogen synthase kinase 3 | CNB00720 | 1272 | -9228.1996 | 100 | 100 | 100 | - | - | 99 | 87 | - | 100 | 73 | - | 100 | 100 | 9/13 | 0.1819497 |
| DNA-directed RNA polymerase ii largest subunit, putative (RPB1) | CNE03720 | 5535 | -54837.8043 | 100 | 100 | 100 | - | - | 100 | 98 | - | 99 | 100 | - | 100 | 100 | 9/13 | 0.2865913 |
| DNA replication licensing factor cdc19 (cell division control protein 19) | CNG02380 | 2928 | -29876.1716 | 100 | 100 | 100 | 73 | - | 100 | - | 100 | - | 92 | - | 100 | 94 | 9/13 | 0.3063356 |
| isocitrate lyase | CNH03280 | 1698 | -15133.6988 | 100 | 100 | 100 | - | - | 87 | 80 | 71 | 98 | - | - | 100 | 100 | 9/13 | 0.2597505 |
| DNA-directed RNA polymerase | CNI00420 | 3414 | -31208.3767 | 87 | 100 | 100 | (48) | - | 93 | (63) | 99 | 76 | 76 | (55) | 100 | 100 | 9/13 | 0.2359366 |
| methylenetetrahydrofolate reductase (NADPH) | CNL04820 | 1929 | -16548.0025 | 100 | 100 | 100 | (53) | 85 | 100 | - | 99 | 99 | 99 | - | 100 | - | 9/13 | 0.2302595 |
| ATP dependent DNA helicase | CNB05360 | 2235 | -22405.5341 | 100 | 100 | 100 | - | (24) | 100 | 72 | 79 | 82 | (45) | (2) | 100 | - | 8/13 | 0.2732160 |
| adenosylhomocysteinase | CND00240 | 1347 | -8971.2698 | 98 | 100 | 100 | - | - | 82 | 90 | 76 | - | - | - | 98 | 99 | 8/13 | 0.1546073 |
| DNA-dependent RNA polymerase II RPB140 (RPB2) | CND03540 | 3849 | -33545.1855 | 100 | 100 | 100 | - | - | 100 | 99 | 100 | (62) | - | - | 100 | 96 | 8/13 | 0.2237954 |
| pyruvate carboxylase | CNF00650 | 3729 | -28326.3212 | 100 | 100 | 100 | - | (37) | 92 | (65) | 100 | 100 | - | - | 100 | 100 | 8/13 | 0.1847746 |
| Eukaryotic translation initiation factor 3 subunit 6 | CNL05160 | 1920 | -16255.6032 | 100 | 100 | 100 | - | - | 100 | - | 100 | 100 | - | - | 100 | 99 | 8/13 | 0.2257396 |
| plasma membrane H(+)-ATPase 1 | CNN01260 | 3135 | -20529.9850 | 100 | 100 | 99 | - | - | 100 | 93 | (62) | 100 | 77 | - | 100 | - | 8/13 | 0.1515828 |
| 1,3-beta-glucan synthase | CNN02320 | 5511 | -47328.6072 | 100 | 100 | 100 | - | - | 100 | 100 | 100 | 100 | (46) | - | 100 | - | 8/13 | 0.2236312 |
| mitogen-activated protein kinase | CNC06590 | 1107 | -8324.0754 | 100 | 99 | 97 | - | - | 81 | 99 | (62) | 83 | (43) | - | 98 | (68) | 7/13 | 0.1666310 |
| orotidine monophosphate pyrophosphorylase (URA5) | CNG03730 | 687 | -6763.7318 | 100 | 100 | 100 | 98 | - | 91 | - | - | (53) | (63) | - | 100 | 99 | 7/13 | 0.3037264 |
| vacuolar ATP synthase | CNI01180 | 1587 | -11933.2227 | 100 | 100 | 89 | - | - | (52) | 75 | (37) | 99 | - | - | 100 | 97 | 7/13 | 0.1767209 |
| Ras2 | CNJ01920 | 1101 | -6180.5535 | 99 | 100 | 99 | - | - | 97 | - | 88 | - | - | - | 100 | 99 | 7/13 | 0.1254647 |
| chaperone | CNM01520 | 2139 | -13392.3250 | 100 | 100 | 100 | - | (39) | 100 | - | 96 | - | - | - | 100 | 100 | 7/13 | 0.1363423 |
| citrate synthase | CNA00510 | 1416 | -9234.5688 | 100 | 100 | - | - | (57) | 89 | (52) | - | 93 | 98 | (69) | 100 | - | 6/13 | 0.1478656 |
| actin | CNA04650 | 1161 | -5631.8845 | 98 | 100 | 73 | - | - | - | 74 | (63) | 85 | - | - | 99 | (62) | 6/13 | 0.0915010 |
| alpha tubulin | CNB02810 | 1371 | -7641.2544 | 100 | 97 | 98 | - | (54) | 89 | - | - | - | - | (65) | 100 | 94 | 6/13 | 0.1094242 |
| argininosuccinate lyase | CNC04420 | 1416 | -11523.0058 | 100 | 100 | 88 | 100 | - | - | (31) | - | - | 73 | - | 100 | - | 6/13 | 0.2090371 |
| beta tubulin | CNC03260 | 1377 | -7299.8992 | 100 | 100 | 100 | - | - | 90 | - | - | - | - | - | 92 | - | 5/13 | 0.1023791 |
| adenylyl-sulfate kinase | CNE03380 | 641 | -5714.2900 | 100 | - | 96 | - | - | (57) | 92 | - | (41) | - | - | 100 | 98 | 5/13 | 0.2429367 |
| translation elongation factor 1-α | CNM01300 | 1389 | -7333.6338 | - | 100 | (60) | - | - | 100 | 98 | (39) | - | - | - | 96 | - | 4/13 | 0.0985092 |
| # nodes contained in concatenated tree*2 | 29/30 | 29/30 | 27/30 | 6/30 | 4/30 | 26/30 | 18/30 | 15/30 | 19/30 | 13/30 | 3/30 | 30/30 | 20/30 | |||||
| CDS product | Homolog to: (locus_tag of C. neoformans) | Based on amino acid sequences | ||||||||||||||||
| Positions used | Highest log likelihood | Bootstrap value of each node*1 | # nodes contained in concatenated tree*2 | Divergence within Trichosporonales*4 | ||||||||||||||
| n | o | p | q | r | s | t | u | v | w | x | y | z | ||||||
| phosphatidylinositol 3-kinase TOR1 | CNF03740 | 2388 | -20501.3857 | 100 | 100 | 100 | 100 | 98 | 100 | 93 | 100 | 100 | 100 | 99 | 100 | 100 | 13/13 | 0.1414040 |
| DNA-directed RNA polymerase ii largest subunit, putative (RPB1) | CNE03720 | 1844 | -19055.5663 | 100 | 100 | 100 | 100 | - | 100 | 80 | - | 100 | 85 | 84 | 91 | 100 | 11/13 | 0.1861724 |
| glutamate synthase (NADH) | CNJ02910 | 2174 | -23206.1602 | 100 | 100 | 100 | 100 | (42) | 100 | 80 | 91 | 100 | 100 | (38) | 100 | 100 | 11/13 | 0.1956882 |
| malate synthase | CNH02910 | 546 | -6042.9704 | 100 | 100 | 100 | - | (41) | 97 | 96 | (63) | 91 | 97 | 73 | 100 | 98 | 10/13 | 0.2240399 |
| methylenetetrahydrofolate reductase (NADPH) | CNL04820 | 633 | -5915.2895 | 100 | 100 | 100 | 80 | (59) | 100 | 75 | 100 | 98 | 90 | - | - | 99 | 10/13 | 0.1540453 |
| ATP-binding cassette (ABC) transporter | CND00300 | 643 | -5438.2601 | 97 | 100 | 100 | (40) | - | 99 | 90 | (49) | 100 | 97 | (53) | 98 | 100 | 9/13 | 0.1424313 |
| DNA-directed RNA polymerase | CNI00420 | 1137 | -8524.1458 | 86 | 100 | 100 | (65) | - | 96 | 78 | - | 100 | 96 | - | 99 | 100 | 9/13 | 0.1097242 |
| 1,3-beta-glucan synthase | CNN02320 | 1836 | -17034.1009 | 97 | 100 | 100 | - | - | 100 | 99 | 100 | 100 | (24) | (51) | 100 | 100 | 9/13 | 0.1593036 |
| pyruvate carboxylase | CNF00650 | 1242 | -10659.4494 | 99 | 100 | 100 | - | (42) | (60) | 87 | 100 | 100 | - | - | 100 | 100 | 8/13 | 0.1286247 |
| DNA replication licensing factor cdc19 (cell division control protein 19) | CNG02380 | 975 | -11547.8857 | 97 | 100 | 100 | (60) | - | 96 | - | 100 | 71 | (43) | - | 96 | 100 | 8/13 | 0.2288008 |
| isocitrate lyase | CNH03280 | 565 | -6484.3719 | 99 | 100 | 100 | (64) | - | 94 | - | 82 | 93 | - | - | 98 | 100 | 8/13 | 0.2222622 |
| vacuolar ATP synthase | CNI01180 | 528 | -3637.3220 | 96 | 99 | - | (63) | - | 95 | 94 | (53) | 79 | 70 | - | 85 | 100 | 8/13 | 0.0735907 |
| phosphoenolpyruvate carboxykinase | CNI03590 | 555 | -3829.0758 | 97 | 100 | 92 | 85 | - | (44) | - | - | 89 | 97 | (56) | 97 | 100 | 8/13 | 0.0931894 |
| plasma membrane H(+)-ATPase 1 | CNN01260 | 1044 | -8907.8908 | 100 | 100 | 100 | - | (47) | 100 | 77 | (54) | 100 | (62) | - | 98 | 100 | 8/13 | 0.1269335 |
| ATP dependent DNA helicase | CNB05360 | 744 | -7343.5154 | 100 | 100 | 100 | (36) | - | 99 | - | (29) | 95 | (50) | - | 74 | 100 | 7/13 | 0.1617158 |
| adenosylhomocysteinase | CND00240 | 447 | -4136.0745 | (24) | 100 | 91 | - | - | 72 | 93 | 71 | - | - | - | 77 | 100 | 7/13 | 0.1579080 |
| DNA-dependent RNA polymerase II RPB140 (RPB2) | CND03540 | 1280 | -10617.4474 | 99 | 100 | 99 | - | - | 100 | - | (63) | 100 | - | - | 96 | 100 | 7/13 | 0.1122744 |
| orotidine monophosphate pyrophosphorylase (URA5) | CNG03730 | 228 | -2840.2696 | 100 | 99 | 97 | 96 | - | 86 | - | - | (69) | (33) | - | 100 | 100 | 7/13 | 0.2999401 |
| Ras2 | CNJ01920 | 366 | -2531.3792 | 97 | 100 | 94 | (55) | - | 95 | - | 90 | - | - | - | 100 | 100 | 7/13 | 0.0971751 |
| Eukaryotic translation initiation factor 3 subunit 6 | CNL05160 | 639 | -6146.9708 | 97 | 100 | 95 | - | - | 100 | (61) | 76 | 100 | - | - | - | 100 | 7/13 | 0.1704422 |
| chaperone | CNM01520 | 712 | -5502.4940 | 100 | 100 | 99 | - | - | 92 | (59) | 86 | 70 | - | - | (61) | 100 | 7/13 | 0.1150690 |
| glycogen synthase kinase 3 | CNB00720 | 421 | -2686.2647 | 88 | 76 | 95 | - | - | (52) | - | (62) | 100 | - | - | 98 | 100 | 6/13 | 0.0792372 |
| argininosuccinate lyase | CNC04420 | 471 | -4055.3207 | 91 | 100 | 95 | 99 | - | 96 | - | (58) | - | - | (59) | - | 100 | 6/13 | 0.1375764 |
| actin | CNA04650 | 386 | -1520.7293 | 82 | 93 | 84 | - | - | - | - | (69) | 96 | - | - | - | 99 | 5/13 | 0.0254971 |
| beta tubulin | CNC03260 | 458 | -2074.0608 | 93 | 100 | 98 | - | - | (61) | - | 90 | - | - | - | (50) | 100 | 5/13 | 0.0307975 |
| mitogen-activated protein kinase | CNC06590 | 368 | -1562.5243 | 97 | 81 | 100 | (68) | - | 89 | - | - | (63) | (42) | - | (54) | 74 | 5/13 | 0.0313906 |
| adenylyl-sulfate kinase | CNE03380 | 212 | -2039.7504 | 98 | 80 | 77 | - | - | (62) | - | 74 | (49) | - | - | (59) | 97 | 5/13 | 0.1536762 |
| citrate synthase | CNA00510 | 471 | -4170.0870 | 100 | 100 | (67) | - | - | (31) | - | (19) | (49) | (57) | - | 100 | 71 | 4/13 | 0.1482440 |
| translation elongation factor 1-α | CNM01300 | 462 | -2674.2830 | (56) | 100 | - | - | - | 94 | 99 | (44) | - | - | - | - | 97 | 4/13 | 0.0626686 |
| alpha tubulin | CNB02810 | 456 | -2114.6945 | 100 | - | - | - | (48) | 83 | - | - | - | - | (21) | (39) | 89 | 3/13 | 0.0321153 |
| # nodes contained in concatenated tree*2 | 28/30 | 29/30 | 26/30 | 7/30 | 1/30 | 23/30 | 13/30 | 13/30 | 20/30 | 9/30 | 3/30 | 20/30 | 30/30 | |||||
*1, Node names are shown in Fig 1b and 1c. Numerals show the bootstrap value of each node which corresponded to that of the concatenated tree [boldface, more than 70%; (), less than 70%].—indicates that the node on the concatenated tree is not shown in respective CDS tree.
*2, Nodes showing more than 70% bootstrap value (boldface) were treated as "positive".
*3, The number of base substitutions per site from averaging over all sequence pairs are shown. Analyses were conducted using the Kimura 2-parameter model [47]. All ambiguous positions were removed for each sequence pair.
*4, The number of amino acid substitutions per site from averaging over all sequence pairs are shown. Analyses were conducted using the JTT matrix-based model [45]. All ambiguous positions were removed for each sequence pair.