onestopshopfungi - Calonectria

Calonectria De Not., Comm. Soc. Crittog. Ital. 2(fasc.3): 477 (1867)

For synonyms see Index Fungorum (2018)

Background

Calonectria was first introduced based on C. daldiniana in 1867. Calonectria species are pathogenic to a wide range of woody and herbaceous plant hosts in tropical and subtropical areas (Chen et al. 2011; Crous 2002; Lechat et al. 2010; Lombard et al. 2010 a,b; Li et al. 2017). The sexual morphs of Calonectria are characterised by yellow to dark red ascomata, with scaly to warty walls, and clavate, 4–8-spored asci. They produce Cylindrocladium asexual morphs with branched conidiophores, cylindrical, septate conidia, and stipe extensions with terminal vesicles (Crous 2002; Lombard et al. 2010b, 2016; Li et al. 2017).

Classification – Sordariomycetes, Hypocreaomycetidae, Hypocreales, Nectriaceae

Type species – Calonectria pyrochroa (Desm.) Sacc., Michelia 1(no. 3): 308 (1878)

Distribution –– Worldwide

Disease Symptoms – Box blight, Cutting rot, Damping off, Canker, Leaf spots, leaf and shoot blights, Red crown rot, Root rot

Species of Calonectria are capable of causing diseases in all plant parts. Most diseases have been recorded from young plants or recent field plantings. Symptoms vary according to host species, host age or developmental stage, environmental conditions and the Calonectria species itself (Barnes and Linderman 2001). Leaf spots (caused by C. colhounii, C. ilicola, C. indusiata and C. pteridis) first appear as water-soaked lesions turning tan to dark brown, circular or irregular in shape surrounded by a red, dark brown or purple border with a chlorotic zone. Root necrosis is the main symptom of root rot caused by species such as C. crotalariae and C. ilicola (Lombard et al. 2010a, 2011). On conifers, there is necrosis of lateral and primary roots accompanied with blacking and splitting of the root cortex while on hardwoods, there is blackening of the root cortex with longitudinal cracking (Cordell et al. 1975). Lesions may coalesce and completely destroy the root. Crown infection can occur with the spread of root infection leading to stunting, discolouration of foliage, defoliation and plant death (Lombard et al. 2010a; Lombard et al. 2011).

Hosts – Calonectria species are soil-borne pathogens and are mainly associated with forestry, agricultural and horticultural plants, on more than 100 plant families (Chen et al. 2011; Crous et al. 1991; Crous 2002, Gehesquiére et al. 2016; Lombard et al. 2010a, b; Li et al. 2017; Lopes et al. 2018). Calonectria species are less commonly associated with fruit rot as compared to leaf spot and root rot (Diaz et al. 2013; Lopes et al. 2018).

Morphological based identification and diversity

Calonectria species were known by Cylindrocladium names for many years. Cylindrocladium species were commonly found in nature and well-known plant pathogens. Later Calonectria was conserved (Hawksworth 2011; McNeill et al. 2012) over Cylindrocladium by Rossman et al. (2013). Most isolates were identified based on morphology. Later, polyphasic approaches based on morphology and sexual compatibility was used to delimit cryptic species (Schoch et al. 2001; Lombard et al. 2010a, b, 2016) and these studies have revealed that there are many species of Calonectria yet to be discovered (Lombard et al. 2016). Calonectria has been subjected to numerous taxonomic studies and 129 species have been recognized based on both morphological and molecular approaches (Crous and Wingfield 1994; Crous 2002; Lechat et al. 2010; Li et al. 2017; Lombard et al. 2010a, b, 2016; Maharachchikumbura et al. 2015, 2016; Lopes et al. 2018).

Macroconidial dimensions and septation, and shape of the vesicle are the best diagnostic characters for identification of Calonectria (Schoch et al. 2000; Crous 2002; Li et al. 2017). Perithecial colour, ascospore number within the asci, and ascospore septation and dimensions are also important for sexual morph identification (Lombard et al. 2010a). However, perithecia of Calonectria species are morphologically very similar, hence are not useful in identification (Crous and Wingfield 1994; Crous 2002). However, intraspecific variation in vesicle shape and conidial dimensions are commonly used in the identification of Calonectria, which can result in taxonomic confusion (Crous et al. 1998; Lombard et al. 2010b).

Molecular based identification and diversity

Morphological data are essential to supplement DNA sequence data for accurate species identification (Lombard et al. 2016). Earlier studies used ITS gene alone to separate Cylindrocladium species, however, the ITS region contains few informative characters (Crous et al. 1999; Schoch et al. 2001; Lombard et al. 2010b). A genus-wide phylogeny can be inferred using TUB, TEF1-α, cmdA and His3 (Lombard et al. 2016; Crous et al. 2002). The LSU gene also provides little information in resolving species of the genus (Lombard et al. 2010b). This study reconstructs the phylogeny of Calonectria based on analyses of a combined TEF1-α, TUB, cmdA and His3 sequence data. After Lombard et al (2010a), this is the first multigene analysis for all the available Calonectria species. Calonectria species formed two major clades in our phylogenetic analysis, which define morphologically similar groups. Similar results were obtained in the previous study by Lombard et al. (2010b) employing seven gene regions (including additional LSU, ITS and ACT sequence data). However, insufficient data are available for the His3 gene region in GenBank. Therefore, it is difficult to have comparative phylogenetic analyses.

Recommended genetic markers (genus level) – LSU and ITS

Recommended genetic markers (species level) – TUB, TEF1-α, cmdA, His3, ACT

Accepted number of species: There are 399 species epithets in Index Fungorum (2018) under this genus. However, only 283 are accepted.

References: Lombard et al. 2010a, b, c, d, 2016, Maharachchikumbura et al. 2015, 2016 (morphology and phylogeny)

Fig Phylogenetic tree generated by maximum likelihood analysis of combined TEF1-α, TUB, cmdA and His3 sequence data of Calonectria species. Related sequences were obtained from GenBank. One hundred sixty strains are included in the analyses, which comprise 1946 characters including gaps. Tree topology of the ML analysis was similar to the one generated from BI (Figure not shown). The best scoring RAxML tree with a final likelihood value of – 35122.522366 is presented. The matrix had 1231distinct alignment patterns, with 15.02% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.219321, C = 0.325516, G = 0.222910, T = 0.232253; substitution rates AC = 1.329187, AG = 3.755831, AT = 1.528969, CG = 0.930598, CT = 4.519462, GT = 1.000000; gamma distribution shape parameter α = 0.749195. Maximum likelihood bootstrap support (MLBT≥65%) and posterior probabilities (BIPP≥0.90) from Bayesian inference analysis are indicated respectively near the nodes. The ex-type strains are in bold and new isolates in blue. The scale bar indicates 0.06 nucleotide changes per site. The tree is rooted to Curvicladiella cignea.