Fig. 1Multiple sequence alignments ofPhytophthora family 5 -(1,4) glycosyl hydrolase members. A grey background indicates similar residues while a black background indicatesidentical residues. An asterisk symbol indicates positions of catalytic residues.
Table 1 Summary of specific primers used to amplify 11 Phytophthora sojae intron-containing genes.
Scaffold coordinates / Oligonucleotides used for RT-PCR / aT-Ca / Exp.Amplicon sizes b / Introns N. c / Intron size (bp)1 / 10:115186-116665 / F;CTGTCAAGCAGAAGTATC
R;CTGGTGAGTAATGTGTTC / 56 / 1026/719 / 4 / 68/80/76/83
2 / 10:43776-45435 / F;CTCCTTCGGCGTCGTCAC
R;AGTCATCATCTCCACCATTTGTTC / 59 / 1381/1003 / 5 / 76/79/98/67/58
3 / 2:1176920-1177782 / F;AAGACCATCCCCAAGACG
R;CTTCCAGAGAGCGAGCAG / 58.5 / 722/474 / 3 / 84/80/84
4 / 27:189631-190594 / F;TGAACTCAAGTGACCATC
R;TCGTCCACCACAATAATG / 56.6 / 966/639 / 1 / 327
5 / 5:971058-973202 / F;CGAGCCCTTCCTCTTGAC
R;ATGACAGCGTGGTTCTTG / 59.6 / 1288/857 / 5 / 74/129/75/76/77
6 / 25:58997-60472 / F;GGCTCTCACGGTGTTTGC
R;CTTGCGGCGGTTGAACTC / 57.5 / 791/535 / 3 / 80/86/90
7 / 26:433-1879 / F;CAGCACGACCTCAAGAAG
R;CCAATGACGGAGAAGAGC / 57 / 496/419 / 1 / 77
8 / 1:1126677-1131591 / F;TCTCGGTCATCTCCATCTAC
R;CCTTCAGGTTGCCATTGC / 56.9 / 404/327 / 1 / 77
9 / 2:921746-922293 / F;CTCAATGGCTCCATCACG
R;CCTTCCTTCTTCCTGTTCC / 54.9 / 408/245 / 2 / 79/84
10 / 81:119639-120820 / F;AGCATCCGCAAGACATTCG
R;CTCACCGTTCGCCTCCTG / 58.8 / 777/636 / 2 / 74/67
11 / 84:73635-77005 / F;CTCGGGTTCCTCTACTAC
F;TCGTTGTCCAGAATGATG / 58 / 702/608 / 1 / 94
a Annealing temperature
b Expected amplicon size with and without intron sequences
c Number of predicted introns in selected gene
Table 2. Primers used for endoglucanase amplifications.
Gene specific probe primers / Amplicon size (bp) / Complete gene primers / Amplicon size (bp)sEGL-V.1 / F5’-CTCCTCACTACTACAACAC-3’
R5’-CAGAGCAGCAATACCTTC-3’ / 434 / F5’-ATGGAAGCCGCCGAGATCT-3’
F5’-CTCGGAGCCTTCGTCGCTCTCC-3’ / 1750
sEGL-V.2 / F5’-GGCAGACAGAGATGAAGC-3’
R5’-CCGTGATATGGCGATACC-3’ / 669 / F5’-ATGGAGGTCAGCGTCGTTCGG-3’
F5’-GCTGGACGACGAAGACGAC-3’ / 1851
sEGL-V.3 / F5’-GGACTACCAGAGCAAGAAC-3’
R5’-GTGTGGAGACTGATGAGC-3’ / 369 / F5’-ATGGCGGAGGTGTCGCGGCCCATG-3’
F5’-CTCGCTTGAAGAGCCCTCGAC-3’ / 1744
sEGL-V.4 / F5’-TCACTGCGTTCCTGTCTC-3’
R5’-TCATTCGTCCTGCCATCC-3’ / 512 / F5’-ATGCCCGAGGTCAGTCGTGTAGTGC-3’
F5’-ATCATCCTCTTCCTCGAGC-3’ / 1733
sEGL-V.5 / F5’-TGTGTCCTCCAACCTCTG-3’
R5’-GCCGTCGTGTAGTAATGC-3’ / 327 / F5’-ATGCGGGACAACCGCCCCAG-3’
F5’-CCCTTCCTTCTCGAAACACG-3’ / 1959
sEGL-V.6 / F5’-CTCCTCACTACTACAACAC-3’
R5’-GTATCCTCCAGCATAACC-3’ / 305 / F5’-ATGTACGCGGGGAACTCGC-3’
F5’-AACCGCAGTGGCCGTCGCAC-3’ / 1918
sEGL-V.7 / F5’-GAGAGCAACAAGTTCAAC-3’
R5’-TCCACCGAATAAGTAAGC-3’ / 630 / F5’-ATGCCGGCACAACGGGACAC-3’
F5’-GTCTGAACCGGACGAGCCTG-3’ / 1909
sEGL-V.8 / F5’-TACATATCGCTGCTCAAG-3’
R5’-CAGTCGTAGTAGTCGTAG-3’ / 386 / F5’-ATGCGACGTGAACCAGAG-3’
F5’-ACTTGAGCTGGACGAGTCAG-3’ / 1843
sEGL-V.9 / F5’-ATCGCCACCATCTACAAG-3’
R5’-CGCATATTACACAGGAAGG-3’ / 1102 / F5’-TGGCTGTAATAATTGGAC-3’
F5’-R;TCTTCTCTTTCAGTTTCG-3’ / 2252
Intron spanning primers
sEGL-V.5 / F;CGCTGACAAGGACCGATTC-3’
R;CTGATGAGCACGCCGATG-3’ / 717
Individual intron primers
sEGL-V.5
intron I / F5’-CAGATTGCGAACGAAGTC-3’
R5’-CGTCGGAGATGATGATGC-3 / 454
sEGL-V.5 intron II / F5’-CGCTGTTCCTGATTACGG-3
R5’-GTTCTTGCTCTGGTAGTCG-3’ / 284
sEGL-V.5 intron III / F5’-CCGACTACCAGAGCAAGAAC-3’
R5’-ATGAGCACGCCGATGTTG- 3’ / 435