Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

Dhanushka Udayanga,Amy Y Rossman,Lisa A Castlebury,Ekachai Chukeatirote,Kevin D Hyde

doi:10.1007/s13225-014-0297-2

Abstract

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 (ACT), DNA-lyase (Apn2), translation elongation factor 1- α (EF1-α), 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-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.

Highlights

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)
Fungal Diversity (2014) 67:203–229 for defining fungal species was proposed by Taylor et al (2000), based on Avise and Ball’s (1990) genealogical concordance species concept requiring the analysis of several unlinked genes
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)

Summary

Introduction

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). Fungal Diversity (2014) 67:203–229 for defining fungal species was proposed by Taylor et al (2000), based on Avise and Ball’s (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). 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 (O’Donnell et al 2004; Taylor et al 2006; Cai et al 2011; Laurence et al 2014). Species recognition criteria in Diaporthe have evolved from morphology and host associations (Wehmeyer 1933) to the recent use of phylogenetic species recognition (Castlebury et al 2003; Santos and Phillips 2009; Santos et al 2011; Udayanga et al 2012a, b; Gomes et al 2013; Tan et al 2013)

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