Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex
Dhanushka Udayanga
Lisa A. Castlebury
Amy Y. Rossman
Ekachai Chukeatirote
Kevin D. Hyde
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) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
, Kunming 650201,
People's Republic of China
The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer.
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(ACT), DNA-lyase (Apn2), translation elongation factor 1-
(EF1-), beta-tubulin (TUB), calmodulin (CAL), 60s
ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence
of sequence heterogeneity of ITS within D. eres is observed,
which complicates the analysis and may lead to overestimation
of the species diversity. The strict criteria of Genealogical
Concordance Phylogenetic Species Recognition (GCPSR)
were applied to resolve species boundaries based on individual
and combined analyses of other seven genes except the ITS. We
accept nine distinct phylogenetic species including Diaporthe
alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D.
helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are
designated for D. alnea, D. bicincta, D. celastrina, D. eres, D.
helicis and D. pulla. Modern descriptions and illustrations are
provided for these species. Newly designed primers are
introduced to amplify and sequence the Apn2 (DNA- lyase) gene in
Diaporthe. Based on phylogenetic informativeness profiles,
EF1-, Apn2 and HIS genes are recognised as the best markers
for defining species in the D. eres complex.
In the last two decades much progress has been made in the
ability to define fungal species through the use of molecular
data (Hibbett and Taylor 2013; Hyde et al. 2013).
Circumscribing species within cryptic species complexes that
have complicated life histories is essential for determining
patterns of speciation and potential hyperdiversity within a
genus (Bickford et al. 2007; Silva et al. 2012a; Fekete et al.
2012; ODonnell et al. 2013). Genealogical Concordance
Phylogenetic Species Recognition (GCPSR) as an approach
for defining fungal species was proposed by Taylor et al.
(2000), based on Avise and Balls (1990) genealogical
concordance species concept requiring the analysis of several unlinked
genes. This approach is often used as an alternative to
morphological and biological species recognition (Dettman et al.
2003a). However, there have been relatively a few evaluations
of the utility of genes to delineate closely related species in
genera with broad host ranges and wide geographic
distributions (Giraud et al. 2008; Dupis et al. 2012; Groenewald et al.
2013; Wikee et al. 2013; Salgado-Salazar et al. 2013).
The principles of GCPSR are based on the assumption that
recombination within a lineage is likely to be the reason for
conflict within gene trees, with the transition from conflict to
congruence representing the species boundaries (Taylor et al.
2000). Selecting multiple genes with strong phylogenetic
signals, the absence of significant incongruence and the
application of standard criteria to determine the species boundaries are
important factors in the best practices of resolving species
complexes (ODonnell et al. 2000; Bischoff et al. 2009;
Watanabe et al. 2011; Salichos and Rokas 2013; Damm et al.
2013; Quaedvlieg et al. 2014). Dettman et al. (2003a) further
upgraded the operational criteria of GCPSR with the
implementation of a two-step process to resolve complex species
level phylogenies in fungi. Independent evolutionary lineages
are recognised by genealogical concordance and
nondiscordance, and subsequently these lineages are subjected to
the ranking based on genetic differentiation and exhaustive
subdivision process to determine the species limits (Dettman
et al. 2003a, b). These methods have been implemented in
species complexes including the model ascomycete
Neurospora (Dettman et al. 2003b, 2006) and some important
plant pathogenic fungal genera (ODonnell et al. 2004; Taylor
et al. 2006; Cai et al. 2011; Laurence et al. 2014). The genus
Diaporthe comprises pathogenic, endophytic and saprobic
species with both temperate and tropical geographic distributions
(Rehner and Uecker 1994; Rossman et al. 2007; Udayanga
et al. 2011; Huang et al. 2013). Species recognition criteria in
Diapo (...truncated)