Evaluation of additional loci
Isolates of Cercospora sp. Q were compared using the five loci used for the combined phylogeny and five additional loci as explained in the Materials and Methods. The results are summarised in Table 3 and detailed per locus below:
ITS--Three allele groups are identified based on sequence identity. The variation in this locus is based on nucleotide changes at only two positions in the second internal transcribed spacer (transitions at positions 451 and 453 compared to the sequence of isolate CPC 5325). Although allele group I was confined to isolates from Cajanus (Fabaceae), the other two groups were intermixed amongst the remaining host genera.
TEF--Two allele groups are identified based on sequence identity. The variation in this locus is based on a single nucleotide change (transitions at position 289 compared to the sequence of isolate CPC 5325). Although allele group I was confined to isolates from Acacia (Fabaceae), Cajanus, and Dioscorea (Dioscoreaceae), the other group represents the remaining host genera.
ACT--Four allele groups are identified based on sequence identity. The variation in this locus is based on nucleotide changes at three positions (transitions at positions 143, 166 and 173 compared to the sequence of isolate CPC 5325). Allele group I was confined to isolates from Cajanus, and allele group II is mainly limited to Dioscorea (except for one isolate from Acacia), allele group IV is limited to the remaining isolates from Acacia, and the remaining host genera belong to allele group III.
CAL--Two allele groups are identified based on sequence identity. The variation in this locus is based on a single nucleotide change (a transition at position 76 compared to the sequence of isolate CPC 5325). This single nucleotide change only occurred in isolate CPC 15844; the rest of the isolates had identical CAL sequences.
HIS--Six allele groups are identified based on sequence identity. The variation in this locus is based on nucleotide changes at 10 positions (transitions at positions 106, 112, 148, 149, 178, 205, 238, 301 and 364, as well as a transversion at position 245 compared to the sequence of isolate CPC 5325). Allele group II differs from allele group I by a unique change of C to T at position 364 and allele group V differs from allele group IV by a unique change of A to T at position 245. Even if allele group I and II and group IV and V are taken as combined groups, isolates from different hosts are intermixed and no clear association of host with allele group, as with the loci mentioned above, is possible.
GAPDH--Six allele groups are identified based on sequence identity. The variation in this locus is based on numerous nucleotide changes (transitions at positions 44, 48-49, 52-53, 56, 63-69, 110, 122, 149, 158, 206, 257, 287, 329, 335, 395, 440, 479, 530, 533, 566, 593, 596, 608, 647, 650, 674, 720, 731, 740, 747, 780, 789, 791-792, 794, 804-806, 808-809, 811-812, 817, 821-822, 824, 830, 834, 837, 839-840, 842-844, 846, 848, 852,...