Colletotrichum: complex species or species ... - CBS - KNAW

Weir et al.Table 2. Primers used in this study, with sequences and sources.Gene Product name Primer Direction Sequence (5’–3’) ReferenceACT Actin ACT-512F Foward ATG TGC AAG GCC GGT TTC GC Carbone & Kohn 1999ACT-783R Reverse TAC GAG TCC TTC TGG CCC AT Carbone & Kohn 1999CAL Calmodulin CL1 Foward GAR TWC AAG GAG GCC TTC TC O’Donnell et al. 2000CL2A Reverse TTT TTG CAT CAT GAG TTG GAC O’Donnell et al. 2000CL1C Foward GAA TTC AAG GAG GCC TTC TC This studyCL2C Reverse CTT CTG CAT CAT GAG CTG GAC This studyCHS-1 Chitin synthase CHS-79F Foward TGG GGC AAG GAT GCT TGG AAG AAG Carbone & Kohn 1999CHS-345R Reverse TGG AAG AAC CAT CTG TGA GAG TTG Carbone & Kohn 1999GAPDH Glyceraldehyde-3-phosphate dehydrogenase GDF Foward GCC GTC AAC GAC CCC TTC ATT GA Templeton et al. 1992GDR Reverse GGG TGG AGT CGT ACT TGA GCA TGT Templeton et al. 1992GS Glutamine synthetase GSF1 Foward ATG GCC GAG TAC ATC TGG Stephenson et al. 1997GSF3 Foward GCC GGT GGA GGA ACC GTC G This studyGSR1 Reverse GAA CCG TCG AAG TTC CAG Stephenson et al. 1997GSR2 Reverse GAA CCG TCG AAG TTC CAC This studyITS Internal transcribed spacer ITS-1F Foward CTT GGT CAT TTA GAG GAA GTA A Gardes & Bruns 1993ITS-4 Reverse TCC TCC GCT TAT TGA TAT GC White et al. 1990SOD2 Manganese-superoxide dismutase SODglo2-F Foward CAG ATC ATG GAG CTG CAC CA Moriwaki & Tsukiboshi 2009SODglo2-R Reverse TAG TAC GCG TGC TCG GAC AT Moriwaki & Tsukiboshi 2009TUB2 β-Tubulin 2 T1 Foward AAC ATG CGT GAG ATT GTA AGT O’Donnell & Cigelnik 1997T2 Reverse TAG TGA CCC TTG GCC CAGT TG O’Donnell & Cigelnik 1997Bt2b Reverse ACC CTC AGT GTA GTG ACC CTT GGC Glass & Donaldson 1995Table 3. Nucleotide substitution models used in phylogeneticanalyses.Gene All taxa Musae clade Kahawae cladeITS TrNef+G TrNef+G TrNefGAPDH HKY+G TPM1uf+G TrNCAL TIM1+G TIM1+G TrN+GACT HKY+G TrN JCCHS-1 TrNef+G TrNef+G K80GS TIM2+G TIM3+GSOD2 HKY+G GTR+I+GTUB2 TrN+G HKY+GConidia were measured and described using conidia taken fromthe conidial ooze on acervuli and mounted in lactic acid, at least24 conidia were measured for each isolate, range measurementsare provided in the form (lower extreme–) 25 % quartile – 75 %quartile (–upper extreme), all ranges were rounded to the nearest0.5 µm. Cultures were examined periodically for the developmentof perithecia. Ascospores were measured and described fromperithecia crushed in lactic acid.Appressoria were producing using a slide culture technique. Asmall square of agar was inoculated on one side with conidia andimmediately covered with a sterile cover slip. After 14 d the coverslip was removed and placed in a drop of lactic acid on a glassslide.All morphological character measurements were analysedwith the statistical programme “R” v. 2.14.0 (R Development CoreTeam 2011). The R package ggplot2 (Wickham 2009) was used forgraphical plots. The box plots show the median, upper and lowerquartiles, and the ‘whisker’ extends to the outlying data, or to amaximum of 1.5× the interquartile range, individual outliers outsidethis range are shown as dots.Taxa treated in the taxonomic sectionSpecies, subspecific taxa, and formae speciales within the C.gloeosporioides species complex are treated alphabetically byepithet. The names of formae speciales are not governed by theInternational Code of Botanical Nomenclature (ICBN) (McNeillet al. 2006, Art. 4, Note 4), and are hence enclosed in quotationmarks to indicate their invalid status. Other invalid names thatare governed by the ICBN are also enclosed in quotation marks.Accepted names are marked with an asterisk (*). The breadth ofthe taxonomic names treated includes:all taxonomic names with DNA sequence data in GenBankthat place them in the C. gloeosporioides complex as it has beendefined here on the basis of the ITS gene tree. The sense that thenames were used in GenBank may have been misapplied;names that have been used in the literature in recent yearsfor which a possible relationship to C. gloeosporioides has beensuggested;all subspecific taxa and formae speciales within C.gloeosporioides and Glomerella cingulata.We have not considered the full set of species in Colletotrichum,Gloeosporium and Glomerella that were placed in synonymy withC. gloeosporioides or Glomerella cingulata by von Arx & Müller(1954) or von Arx (1957, 1970).For each accepted species, comments are provided regardingthe limitations of ITS, the official barcoding gene for fungi, todistinguish that species from others within the C. gloeosporioidescomplex.124