Diaporthe

Background

Diaporthe (=Phomopsis) is a cosmopolitan genus of fungi comprised of endophytes, plant pathogens, and saprobes occurring on a wide range of annual and perennial hosts, including economically important crops (Uecker 1988; Farr and Rossman 2014; Udayanga et al. 2011). The genus belongs to class Sordariomycetes, order Diaporthales, and the family Diaporthaceae, typified by the species Diaporthe eres Nitschke (Wehmeyer 1933). With the change to one scientific name for fungi (McNeill et al. 2012), Diaporthe has priority, being the older generic name compared to Phomopsis. Many species are able to colonize diverse hosts as opportunists; some species are host specific and multiple species can even co-occur on the same host (Mostert et al. 2001; Farr et al. 2002a; Crous and Groenewald 2005). Species of Diaporthe cause cankers, diebacks, root rots, fruit rots, leaf spots, blights and wilts on a wide range of plant hosts including some economically important hosts and have been the subject of considerable phytopathological research. Examples of diseases on major crops include Diaporthe/Phomopsis complex causing soybean seed decay, pod and stem blight and cankers, sunflower stem canker (D. helianthi), dead arm of grapevines (D. ampelina) and melanosis in Citrus (D. citri) (Van Niekerk et al. 2005; Santos et al. 2011; Thompson et al. 2011; Udayanga et al. 2014a, b). In addition, several species of Diaporthe are known from clinical reports of immunocompromised patients, although these pathogens are only provisionally identified to species level (Garcia-Reyne et al. 2011; Mattei et al. 2013). Diaporthe comprises a major component of endophytes in tropical and temperate trees, and several species have been used in secondary metabolite research (Isaka et al. 2001; Li et al. 2010a, b; Kaul et al. 2012).

Species identification and numbers

The Genealogical Concordance Phylogenetic Species Recognition (GCPSR) has been applied in the genus Diaporthe to define the species boundaries in recent studies (Udayanga et al. 2012b; Gomes et al. 2013; Tan et al. 2012). Therefore species delimitation is currently based on DNA sequence data and comparison of morphological characters (Santos and Phillips 2009; Santos et al. 2010; Diogo et al. 2010; Udayanga et al. 2014a, b). Although the genus Diaporthe has received much attention, few phylogenetic studies have thus far been conducted; hence the taxonomy of some of the species in this genus is still uncertain including many of the common plant pathogens. Index Fungorum lists 892 Diaporthe names and 983 Phomopsis names whereas MycoBank (2014) lists 919 Diaporthe names and 1,040 Phomopsis names. However, the names available in the literature are mostly applied based on host association and morphology except fewer species described in the last two decades based on DNA sequence data. Ex-type cultures are available for less than 100 species known despite a large number of species listed in databases and literature. The delimitation of species within the genus Diaporthe improved once DNA sequence data were incorporated (Castlebury and Mengistu 2006; Van Rensburg et al. 2006; Santos et al. 2010; Udayanga et al. 2012b, 2014a, b) since this facilitates obtaining detailed insight into complex evolutionary relationships.

Molecular phylogeny

Since the first molecular phylogenetic study in Diaporthe (Rehner and Uecker 1994), rDNA ITS, partial sequences  of translation elongation factor 1-α (TEF) and  mating  type genes (MAT 1-1-1/1-2-1) have commonly been used in molecular phylogenetic studies in this genus (Van Niekerk et al. 2005;  Van  Rensburg  et  al.  2006;  Santos et al. 2010; Udayanga et al. 2011; Sun et al. 2012). Udayanga et al. (2012a) used ITS, TEF, β- tubulin and CAL genes with a selected set of ex-type cultures and additional isolates to infer the phylogeny of the genus. In a parallel study, a multi-marker phylogeny was effectively used to describe novel species in Diaporthe based on fresh collections from Thailand (Udayanga et al. 2012b). Gomes et al. (2013) used a Brazilian collection of isolates and existing ex-type cultures for a combined phylogenetic analysis of five genetic markers which included ITS, TEF, β- tubulin, CAL and HIS. They introduced several novel taxa from Brazilian collections from medicinal plants with one epitype for Diaporthe anarcardi from Kenya. Udayanga et al. (2014a, b) revisited the Diaporthe species associated with Citrus worldwide with a comprehensive assessment of the genes including ITS, TEF, β- tubulin, CAL and ACT. The study revisited several important phytopathogens including  D.  citri,  D.  cytosporella,  D.  forniculina  and D. rudis, with the epitypes designated with modern The clarification of  D. foeniculaina and D. rudis revealed the potential extensive host association of some species.

Udayanga et al. (2014a) further emphasized that ITS alone can cause much confusion in defining closely related taxa, which has also been noted by several previous researchers regarding closely related species in Diaporthe (Farr et al. 2002a, b; Murali et al. 2006; Santos et al. 2010). The variation of ITS sequences can result in superfluous, multiple terminal branches in combined analyses, even when other gene regions do not support these distinctions (Udayanga et al. 2014a, b). The TEF gene is informative when it comes to clarifying species limits in Diaporthe (Table, Fig.).