Alternaria Nees, Syst. Pilze (Würzburg): 72 (1817).
Index Fungorum number: IF 7106; Facesoffungi number: FoF 00501, 589 morphological species (Species Fungorum 2022), >50 species with molecular data.
Pathogenic on host. Sexual morph: Ascomata small, solitary to clustered, erumpent to (nearly) superficial at maturity, globose to ovoid, dark brown, smooth, apically papillate, ostiolate. Ostiole papilla short, blunt. Peridium relatively thin. Hamathecium of cellular pseudoparaphyses. Asci (4–6–) 8- spored, bitunicate, fissitunicate, cylindrical to cylindroclavate, straight or somewhat curved, with a short, furcate pedicel and minute ocular chamber. Ascospores ellipsoid to fusoid, muriform, slightly constricted at septa, yellow-brown, without guttules, smooth-walled. Asexual morph: Stroma rarely formed, setae and hyphopodia absent. Conidiophores macronematous, mononematous, simple or irregularly and loosely branched, pale brown or brown, solitary or in fascicles. Conidiogenous cells integrated, terminal becoming intercalary, polytretic, sympodial, or sometimes monotretic, cicatrized. Conidia catenate or solitary, dry, ovoid, obovoid, cylindrical, narrowly ellipsoid or obclavate, beaked or nonbeaked, pale or medium olivaceous-brown to brown, smooth or verrucose, with transverse and with or without oblique or longitudinal septa (Adapted from Woudenberg et al. 2013 and Ariyawansa et al. 2015).
Type species: Alternaria tenuis Nees
Notes: Alternaria is characterised by solitary to clustered, erumpent to superficial ascomata, cylindrical to cylindro-clavate asci and ellipsoid to fusoid, muriform ascospores. Previously, the taxonomy of Alternaria was unreliable because it was based solely on general morphological characters or host specificity. Later studies used several morphological characters of conidia and a three-dimensional sporulation arrangement which led to identification of numerous Alternaria species groups (Simmons 1992, 1993, 1995). Far along, various Alternaria species were grouped into sections, as taxa of the sub-generic rank. Currently, a total of 275 Alternaria species, divided into 26 subgeneric sections are recognized based on morphology and phylogenetic evidence (Simmons 2007; Dettman and Eggertson 2021).The phylogenetic analyses of Woudenberg et al. (2013) based on SSU, LSU, ITS, GAPDH, RPB2 and TEF1 revealed that multiple paraphyletic genera exist within the Alternaria complex and several clades do not relate to the species-groups based on morphological characteristics. Woudenberg et al. (2013) synonymized thirteen genera namely Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces under Alternaria s. str., thereby expanding the generic concept of the genus. This treatment was followed by subsequent authors (Ariyawansa et al. 2015; Li et al. 2022). Ariyawansa et al. (2015) described the sexual morph of Alternaria alternata from Italy and added a new species A. murispora but did not obtain the asexual morph from cultures and provided a phylogenetic tree of Alternaria based on ITS, SSU, LSU and RPB2 sequence data. The phylogenetic relationships within species groups often varies with the morphological characters used to demarcate morphospecies. Several molecular approaches have been suggested for delineating the Alternaria sections such as the random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) (Dini-Andreote et al. 2009), selective subtractive hybridisation (García-Coronado et al. 2015) and sequence characterized amplified genomic regions (Stewart et al. 2013). However, none of these methods effectively differentiated all morphospecies within sections such as sect. Alternaria (Li et al. 2022). Since the introduction of next generation sequencing (NGS), many studies have used whole-genome sequencing technologies to search for genes that can differentiate among the described species (Lawrence et al. 2013; Woudenberg et al. 2015). Woudenberg et al. (2015) used multi-gene phylogeny based on combined ITS, GAPDH, RPB2, TEF-1, Alt-a1, endoPG and OPA10-2 gene loci coupled with whole-genome and transcriptome comparisons to delineate species in sect. Alternaria. Li et al. (2022) discussed the species limits, evolution and provided an updated multigene phylogeny based on combined SSU, LSU, RPB2, ITS, GAPDH, TEF1, Alt-a1 and gave a taxonomic explanation on the classification of Alternaria. Li et al. (2022) pointed out that there is a lack of phylogenetic effective coding genes which makes identification of Alternaria species tedious and there is need to re-define and expand the generic concept of Alternaria sections. Several authors added new species to Alternaria (Zhang et al. 2003; Simmons and Hill 2007; Marin-Felix et al. 2019; Li et al. 2022). Alternaria is a distinct but complex genus in Pleosporaceae. Molecular markers available for Alternaria include ITS, LSU, SSU, TEF1, RPB2, GAPDH and Alt-a1. Currently, ITS, ATP, and GAPDH genes are most reliable to delineate species of Alternaria (Woudenberg et al. 2015; Dettman and Eggertson 2021).
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