Pleosporales - CBS - KNAW

Fungal Diversity
2. To investigate the phylogeny of Pleosporales, its interfamilial
relationships, and the morphological circumscription
of each family;
In order to clarify morphological characters, the generic
types of the majority of teleomorphic pleosporalean genera
(> 60%) were studied. Most of them are from the “core
families” of Pleosporales, i.e.Delitschiaceae, Lophiostomataceae,
Massariaceae, Massarinaceae, Melanommataceae,
Montagnulaceae, Phaeosphaeriaceae, Phaeotrichaceae, Pleomassariaceae,
Pleosporaceae, Sporormiaceae and Teichosporaceae.
Notes are given for those where type
specimens could not be obtained during the timeframe
of this study. A detailed description and illustration of
each generic type is provided. Comments, notes and
problems that need to be addressed are provided for each
genus. Phylogenetic investigation based on five nuclear loci,
viz. LSU, SSU, RPB1, RPB2 andTEF1 was carried out using
available strains from numerous genera in Pleosporales. In
total, 278 pleosporalean taxa are included in the phylogenetic
analysis, which form 25 familial clades on the dendrogram
(Plate 1). The suborder, Massarineae, is emended to
accommodate Lentitheciaceae, Massarinaceae, Montagnulaceae,
Morosphaeriaceae and Trematosphaeriaceae.
Materials and methods
Molecular phylogeny
Four genes were used in this analysis, the large and small
subunits of the nuclear ribosomal RNA genes (LSU, SSU)
and two protein coding genes, namely the second largest
subunit of RNA polymerase II (RPB2) and translation
elongation factor-1 alpha (TEF1). All sequences were
downloaded from GenBank as listed in Table 3. Eachof
the individual ribosomal genes was aligned in SATé under
default settings with at least 20 iterations. The protein coding
genes were aligned in BioEdit (Hall 2004) and completed by
manual adjustment. Introns were removed and all genes were
concatenated in a single nucleotide alignment with 43%
missing and gap characters out of a total set of 5081. The
alignment had 100% representation for LSU, 75% for SSU,
48% for RPB2 and65%forTEF1. The final data matrix had
280 taxa including outgroups (Table 3).
Previous results indicated no clear conflict amongst the
majority of the data used (Schoch et al. 2009). A phylogenetic
analysis of the concatenated alignment was performed on
CIPRES webportal (Miller et al. 2009) using RAxML v. 7.2.7
(Stamatakis 2006; Stamatakis et al. 2008) applying unique
model parameters for each gene and codon (8 partitions). A
general time reversible model (GTR) was applied with a
discrete gamma distribution and four rate classes. Fifty
thorough maximum likelihood (ML) tree searches were done
in RAxML v. 7.2.7 under the same model, each one starting
from a separate randomized tree and the best scoring tree
selected with a final likelihood value of −95238.628839. Two
isolates of Hysterium angustatum (Hysteriales, Pleosporomycetidae)
were used as outgroups based on earlier work
(Boehm et al. 2009a). Bootstrap pseudo-replicates were run
with the GTRCAT model approximation, allowing the
program to halt bootstraps automatically under the majority
rule criterion (Pattengale et al. 2010). The resulting 250
replicates were plotted on to the best scoring tree obtained
previously. The phylogram with bootstrap values on the
branches is presented in Plate 1 by using graphical options
available in TreeDyn v. 198.3 (Chevenet et al. 2006).
Morphology
Type specimens as well as some other specimens were loaned
from the following herbaria: BAFC, BISH, BPI, BR, BRIP,
CBS, E, ETH, FFE, FH, G, H, Herb. J. Kohlmeyer, HHUF,
IFRD, ILLS, IMI, K(M), L, LPS, M, MA, NY, PAD, PC, PH,
RO, S, TNS, TRTC, UB, UBC, UPS and ZT. Attempts were
made to trace and borrow all the type specimens from herbaria
worldwide, but only some of them could be obtained. Some of
the type specimens are in such bad condition that little
information could be obtained. In order to obtain the location
of specimens, original publications were searched.
Ascostroma and ascomata were examined under an
Olympus SZ H10 dissecting microscope. Section of the
fruiting structures was carried out by cryotome or by handcutting.
Measurements and descriptions of sections of the
ascomata, hamathecium, asci and ascospores were carried out
by immersing ascomata in water or in 10% lactic acid.
Microphotography was taken with material mounted in water,
cotton blue, Melzer’s reagent or 10–100% lactic acid.
Terminologies are as in Ulloa and Hanlin (2000). In
addition, ascomata size is defined as: small-sized: < 300 μm
diam., medium-sized: from 300 μm to 600 μm diam., largesized:
> 600 μm diam.
Question mark (“?”) before family (or genus) name
means its familial (or generic) status within Pleosporales
(or some particular family) is uncertain. Other question
marks after habitats, latin names or other substantives mean
the correctness of their usages need verification.
Results
Molecular phylogeny
In total, 278 pleosporalean taxa are included in the phylogenetic
analysis. These form 25 familial clades in the dendrogram,
i.e. Aigialaceae, Amniculicolaceae, Arthopyreniaceae,