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

The Colletotrichum gloeosporioides species complex
Table 1. (Continued).
Species Culture* Host Country GenBank accession number
ITS GAPDH CAL ACT CHS-1 GS SOD2 TUB2
C. ti ICMP 5285 Cordyline australis New Zealand JX010267 JX009910 JX009650 JX009553 JX009897 JX010124 JX010363 JX010441
ICMP 4832* Cordyline sp. New Zealand JX010269 JX009952 JX009649 JX009520 JX009898 JX010123 JX010362 JX010442
C. tropicale MAFF 239933, ICMP 18672 Litchi chinensis Japan JX010275 JX010020 JX009722 JX009480 JX009826 JX010086 JX010318 JX010396
CBS 124949*, ICMP 18653 Theobroma cacao Panama JX010264 JX010007 JX009719 JX009489 JX009870 JX010097 JX010329 JX010407
CBS 124943, ICMP 18651 Annona muricata Panama JX010277 JX010014 JX009720 JX009570 JX009868
Xanthorrhoea preissii Australia JX010261 JX009927 JX009653 JX009478 JX009823 JX010138 JX010369 JX010448
C. xanthorrhoeae BRIP 45094*, ICMP 17903,
CBS 127831
IMI 350817a, ICMP 17820 Xanthorrhoea sp. Australia JX010260 JX010008 JX009652 JX009479 JX009814
Glomerella cingulata “f.sp. camelliae” ICMP 10643 Camellia × williamsii UK JX010224 JX009908 JX009630 JX009540 JX009891 JX010119 JX010358 JX010436
ICMP 18542 Camellia sasanqua USA JX010223 JX009994 JX009628 JX009488 JX009857 JX010118 JX010357 JX010429
ICMP 10646 Camellia sasanqua USA JX010225 JX009993 JX009629 JX009563 JX009892 JX010117 JX010359 JX010437
* = ex-type or authentic culture, (*) = ex-type or authentic culture of synonymised taxon. Sequences downloaded from GenBank, not generated as part of this project are in bold font. Collection abbreviations are listed in the methods.
Several species-trees analyses were conducted using BEAST
v. 1.7.1 (Drummond et al. 2012). Species-trees combine multi-gene
and multiple isolate data to reconstruct the evolutionary history
of hypothesised species, rather than individual isolates. BEAST
does not use concatenation, but rather co-estimates the individual
gene trees embedded inside the summary species tree. It also
estimates the time since each species shared a common ancestor
(divergence times). For these analyses the species tree ancestral
reconstruction option was selected (Heled & Drummond 2010), the
gene data partitioned as for BI and the substitution model for each
gene was selected based on the models selected using jModelTest.
The individual isolates were grouped into sets of species by setting
species names as trait values. A strict clock was used for the
GAPDH gene (as an all intronic sequence it was assumed to be
accumulating mutations at a steady rate) and the other gene clock
rates were estimated relative to GAPDH, using an uncorrelated
lognormal relaxed clock. The species tree prior used for all genes
was the Yule process, with the ploidy type set to nuclear autosomal.
Uninformative priors were used for all parameters, and were
allowed to auto optimise.
The first species-tree analysis was conducted using the 158
isolate, five gene dataset, with C. boninense and C. hippeastri as
the outgroups. The MCMC chain was set to 1 × 10 8 generations
for the species complex tree and samples were taken from the
posterior every 1000 generations. The analysis was run twice
independently. The effective sample size (ESS) and traces of
all parameters and convergence of the two runs was checked
with Tracer and a summary maximum clade credibility species
tree was built with TreeAnnotator v. 1.7.1 (Drummond et al.
2012) using a 10 % burn-in and a posterior probability limit of
0.5, setting the heights of each node in the tree to the mean
height across the entire sample of trees for that clade. Separate
analyses were conducted using all eight genes and the same
restricted set of isolates chosen to represent taxa within the
Musae clade and the Kahawae clade as were used for the BI
analyses of the eight gene concatenated analyses outlined
above. For each of the Musae and Kahawae clade analyses,
the MCMC chain was set to 5 × 10 7 generations, but otherwise
run as for the five gene dataset.
To illustrate the potential limitations of ITS to discriminate species
within the C. gloeosporioides complex, an UPGMA tree was built
of all 158 ITS sequences, using the Geneious tree builder tool. A
UPGMA tree visually approximates a BLAST search, which is based
on distances (and sequence length) rather than corrected nucleotide
substitutions of more sophisticated, model-based analyses.
Sequences derived in this study were lodged in GenBank (Table
1), the concatenated alignment and trees in TreeBASE (www.
treebase.org) study number S12535, and taxonomic novelties in
MycoBank (Crous et al. 2004).
Morphology
Detailed morphological descriptions are provided only for those
species with no recently published description. Few specimens
were examined from infected host material; the descriptions
provided are mostly from agar cultures. Cultures were grown on
Difco PDA from single conidia, or from single hyphal tips for the few
specimens where no conidia were formed, with culture diameter
measured and appearance described after 10 d growth at 18–20 o C
under mixed white and UV fluorescent tubes, 12 h light/12 h dark.
Colour codes follow Kornerup & Wanscher (1963).
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