Figures (29)  Tables (6)
    • Figure 1. 

      Phylogenetic construction of Pleosporales using RAxML-based maximum likelihood analysis of a combined ITS, LSU, SSU, TEF1-α and RPB2 DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 70% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 PP are shown above the nodes. The tree is rooted to Arthoniomycetes (Arthonia dispersa UPSC2583, Dendrographa leucophaea f-minor, Roccella fuciformis Tehler 8171 and Schismatomma decolorans Ertz 5003). The type strains are indicated by boldface 'T'.

    • Figure 2. 

      Maximum clade credibility (MCC) tree with divergence times estimates obtained from BEAST. Numbers in red indicate the fossil (1, 2) and secondary (3) points. Numbers in blue indicate divergence time estimate of Pleosporales (stem age: 5, crown age: 4). Letters in purple indicate divergence time estimate of Alternaria (stem age: A, crown age: B). Single lineages of Alternaria species are highlighted in blue.

    • Figure 3. 

      Phylogenetic construction of genus Alternaria using RAxML-based maximum likelihood analysis of a combined ITS, LSU, SSU, TEF1-α, RPB2, GAPDH and Alt-a1 DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 70% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 PP are shown above the nodes. The tree is rooted to Stemphylium vesicarium (CBS 191.86) and Pleospora tarda (CBS 714.68). Newly generated strains are in blue. The type strains obtained from ex-type cultures are indicated by 'T' and the type strains obtained from specimens are indicated by 'H'.

    • Figure 4. 

      Phylogenetic construction of Alternaria alternata using RAxML-based analysis of a combined ITS, LSU, SSU, TEF1-α, RPB2, GAPDH and Alt-a1 DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 60% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 are shown above the nodes. The tree is rooted to Alternaria eichhorniae (CBS 489.92) and Alternaria eichhorniae (CBS 119778). Newly generated strains are in blue, and the type strains are indicated by 'T'.

    • Figure 5. 

      Phylogenetic construction of Alternaria sect. Infectoriae using RAxML-based analysis of a combined ITS, GAPDH and ATPase DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 70% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 PP are shown above the nodes. The tree is rooted with taxa in sect. Chalastospora (Alternaria malorum CBS 135.31 and A. abundans CBS 534.83). Newly generated strains are in blue. The type strains obtained from ex-type cultures are indicated by 'T' and the type strains obtained from specimens are indicated by 'H'.

    • Figure 6. 

      Phylogenetic construction of Alternaria sect. Porri using RAxML-based analysis of a combined ITS, GAPDH, TEF1-α, RPB2 and Alt-a1 DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 70% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 PP are shown at the nodes. The tree is rooted to sect. Gypsophilae (Alternaria gypsophilae CBS 107.41). Newly generated strains are in blue and the type strains are indicated by 'T'.

    • Figure 7. 

      Phylogenetic construction of Alternaria sect. Radicina using RAxML-based analysis of a combined ITS, TEF1-α, GAPDH and Alt-a1 DNA sequence dataset. Bootstrap support values for maximum likelihood (ML, black) equal to or greater than 60% and Bayesian posterior probabilities (PP, red) equal to or greater than 0.95 PP are shown above the nodes. The tree is rooted to A. helianthiinficiens (CBS 208.86 and CBS 117370). Newly generated strains are in blue. The type strains obtained from ex-type culture are indicated by 'T' and the type strains obtained from holotype specimen are indicated by 'H'.

    • Figure 8. 

      Sporulation in Alternaria spp. (a) A. eupatoriicola (MFLU 21-0319). (b) A. lathyri (MFLU 21-0297). (c) A. oblongoellipsoidea (MFLU 21-0310). (d) A. macilenta (MFLU 21-0305). (e) A. baoshanensis (MFLU 21-0296). (f) A. falcata (MFLU 21-0306). (g) A. ellipsoidialis (MFLU 21-0307). (h) A. arctoseptata. (i) A. salicicola (MFLU 21-0320). (j) A. arundinis (MFLU 21-0313). (k) A. phytolaccae (MFLU 21-0314). (l) A. breviconidiophora (MFLU 21-0317). (m) A. phragmiticola (MFLU 21-0316). (n) A. minimispora (MFLU 21-0295). Scale bars: (a)–(n) = 10 µm.

    • Figure 9. 

      Alternaria alternata (MFLU 21-0302). (a), (b) Colonies on dead branch. (c)–(i) Conidiophores. (j)–(u) Conidia. Scale bars: (a) = 0.1 cm, (b) = 300 µm, (c)–(u) = 20 µm.

    • Figure 10. 

      Alternaria arctoseptata (MFLU 21-0308, holotype). (a) Colonies on dead stem of Lathyrus sp. (Fabaceae). (b)–(g) Conidiophores bearing conidiogenous cells. (h), (i) Immature conidia. (j), (o) Conidia formed secondary conidiophores. (k)–(n) Mature conidia. Scale bars: (a) = 200 µm, (b)–(o) = 20 µm.

    • Figure 11. 

      Alternaria baoshanensis (MFLU 21-0296, holotype). (a) Colonies on dead rattan of Curcubita moschata. (b)–(e) Conidiophores with a distinct conidiogenous locus. (f)–(l) Variation in shape of conidia. Scale bars: (a) = 200 µm, (b)–(e) = 30 µm, (f)–(l) = 20 µm.

    • Figure 12. 

      Alternaria breviconidiophora (MFLU 21-0317, holotype). (a) Colonies on dead branch. (b) Conidiophores arising on stomatic base. (c)–(g) Conidiophores. (h)–(q) Conidia. Scale bars: (a) = 50 µm, (b)–(g) = 20 µm, (h)–(q) = 10 µm.

    • Figure 13. 

      Alternaria doliconidium (MFLU 21-0294). (a) Dead stem of Reseda sp. (Resdaceae). (b) Colonies on dead stem. (c)–(j) Conidiophores on natural substrate. (k)–(m) Conidiogenesis sporulated in vitro. (n) Germinated conidium. (o)–(r) Conidia ((q), (r) on natural substrate)). Scale bars: (a) = 0.1 cm, (b) = 500 µm, (c)–(r) = 20 µm.

    • Figure 14. 

      Alternaria ellipsoidialis (MFLU 21-0307, holotype). (a) Colonies on dead hulls of Brassica sp. (b)–(g) Conidiophores bearing conidiogenous cells with a few apical conidiogenous loci. (h)–(q) Conidia. Scale bars: (a) = 300 µm, (b)–(g) = 30 µm, (h)–(q) = 20 µm.

    • Figure 15. 

      Alternaria eupatoriicola (MFLU 21-0319, holotype). (a) Colonies on dead hanging stem of Eupatorium cannabinum. (b)–(f) Conidiophores bearing conidiogenous cells. (g)–(q) Conidia. Scale bars: (a) = 300 µm, (b)–(m) = 20 µm.

    • Figure 16. 

      Alternaria falcata (MFLU 21-0306, holotype). (a) Colonies on dead hanging stem of Atriplex sp. (b)–(g) Conidiophores bearing conidiogenous cells. (h)–(m) Conidia. Scale bars: (a) = 150 µm, (b)–(m) = 20 µm.

    • Figure 17. 

      Alternaria lathyri (MFLU 21-0297, holotype). (a) Colonies on dead stem dead aerial stem of Lathyrus sp. (b) Conidiophores and conidia. (c)–(h) Conidiophores bearing conidiogenous cells. (i)–(n) Conidia. (o) Germinated conidium. Scale bars: (a) = 200 µm, (b)–(o) = 20 µm.

    • Figure 18. 

      Alternaria macilenta (MFLU 21-0305, holotype). (a) Colonies on dead stem of Scabiosa sp. (b)–(g) Conidiophores. (h)–(l) Conidia. Scale bars: (a) = 150 µm, (b)–(l) = 20 µm.

    • Figure 19. 

      Alternaria macroconidia (MFLU 21-0301, holotype). (a) Specimen examined of Spartium junceum (Fabaceae). (b) Colonies on dead aerial branch of Spartium junceum. (c)–(j) Conidiophores bearing conidiogenous cells. (k)–(n) Immature conidia. (o)–(s) Mature conidia. (t) Germinated conidium. Scale bars: (a) = 0.5 cm, (b) = 1000 µm, (c)–(t) = 20 µm.

    • Figure 20. 

      Alternaria minimispora (MFLU 21-0295, holotype). (a) Colonies on rotten peel of Citrullus lanatus. (b)–(e), (h), (i) Conidiophores bearing conidiogenous cells. (f) Conidiogenous cells. (g) Secondary conidiophores arising from conidia. (j)–(q) Conidia. Scale bars: (a) = 300 µm, (b)–(e), (h), (i) = 30 µm, (f), (g), (j)–(q) = 10 µm.

    • Figure 21. 

      Alternaria oblongoellipsoidea (MFLU 21-0310, holotype). (a) Colonies on dead stem of Cichorium intybus. (b)–(h) Conidiophores bearing conidiogenous cells. (i)–(l) Conidia. (m) Germinated conidium. Scale bars: (a) = 300 µm, (b)–(m) = 20 µm.

    • Figure 22. 

      Alternaria orobanches (MFLU 21-0303, holotype). (a) Colonies on dead stem of Orobanche sp. (b)–(g) Conidiophores bearing conidiogenous cells. (h) Conidiophores bearing conidiogenous cells with attached conidia. (i)–(q) Conidia. (r) Germinated conidium. Scale bars: (a) = 100 µm, (b)–(r) = 20 µm.

    • Figure 23. 

      Alternaria phragmiticola (MFLU 21-0316, holotype). (a) Colonies on dead stem Phragmites sp. (b)–(g) Conidiophores bearing conidiogenous cells. (h)–(o) Conidia. Scale bars: (a) = 200 µm, (b)–(o) = 20 µm.

    • Figure 24. 

      Alternaria salicicola (MFLU 21-0320, holotype). (a) Colonies on dead twig of Salix alba. (b)–(e) Conidiophores bearing conidiogenous cells. (f)–(p) Conidia. (q) Germinated conidium. Scale bars: (a) = 150 µm, (b)–(q) = 20 µm.

    • Figure 25. 

      Alternaria arundinis (MFLU 21-0313, holotype). (a) Colonies on dead stem of Arundo donax. (b)–(f) Conidiophores bearing conidiogenous cells. (g)–(i) Conidia formed secondary conidiophores. (j)–(n) Conidia. Scale bars: (a) = 150 µm, (b)–(n) = 20 µm.

    • Figure 26. 

      Alternaria nodulariconidiophora (MFLU 21-0315, holotype). (a) Colonies on dead stem of Heracleum sphondylium. (b)–(e) Geniculate conidiophores bearing conidiogenous cells. (f)–(m) Conidia. (n) Germinated conidium. Scale bars: (a) = 100 µm, (b)–(n) = 20 µm.

    • Figure 27. 

      Alternaria nodulariconidiophora (MFLUCC 21-0131) sporulated on PDA. (a) Conidium formed a geniculate secondary conidiophore. (b), (c) Secondary conidiophores bearing conidia with three-dimensional branching patterns. Scale bars: (a)–(c) = 30 µm.

    • Figure 28. 

      Alternaria brevirostra (MFLU 21-0312, holotype). (a) Colonies on dead stem of Plantago sp. (b)–(f) Conidiophores bearing conidiogenous cells. (g)–(k) Conidia. (l) Germinated conidium. Scale bars: (a) = 100 µm, (b)–(l) = 20 µm.

    • Figure 29. 

      Alternaria phytolaccae (MFLUCC 21-0314, holotype). (a) Colonies on dead standing stem of Phytolacca sp. (b)–(e) Conidiophores bearing conidiogenous cells, with 2–3 conidiogenous loci on side of cell. (f), (g) Immature conidia. (h)–(k) Conidia. Scale bars: (a) = 150 µm, (b)–(k) = 20 µm.

    • Alternaria sectionsConidiogenesis structuresEcology and economyReferences
      Sect. AlternantheraeConidiophoresShort to moderately long, with slightly enlarged conidiogenous tip.Species in this section are reported as plant pathogens that mainly cause leaf spots.[11,13,15,55]
      ConidiaLarge, ellipsoidal to ovoid, or subcylindrical, rarely narrow ellipsoidal, solitary or rarely paired, disto- and euseptate, transversely septate with no or 1–2 longitudinal or oblique septa, slightly constricted near some septa, with a long apical narrow beak, conidial beak unbranched, septate or aseptate, long filiform, sometimes swollen at the end, internal compartmentation occurs, with cell bright at end, with hexagonal, octagonal or rounded transverse sections lumina.
      Sect. AlternariaConidiophoresShort to long, straight or curved, simple or branched, with one or several apical conidiogenous loci.Species in this section are reported as plant pathogens on leaves, stems and fruits, and vegetables. Some species cause opportunistic infections of humans. Species in this section are also reported as resources of potential toxins and secondary metabolites.[11,12,15,100]
      ConidiaObclavate to long ellipsoid, small or moderate in size, septate, slightly constricted near some septa, with few longitudinal septa, in moderately long to long, simple or branched chains, form tapered beak or secondary conidiophore with one or a few conidiogenous loci.
      Sect. BrassicicolaConidiophoresShort to moderately long, simple or branched, with one or several apical conidiogenous loci.Species in this section mainly cause black spot disease on a wide range of hosts, particularly on Brassica spp. such as cabbage, Chinese cabbage, cauliflower, oilseeds, broccoli and canola. Species in this section are also reported as sources of antibiotic masses.[11,14,101103]
      ConidiaEllipsoid, ovoid or somewhat obclavate, small or moderate in size, septate, slightly or strongly constricted at most of the transverse septa, with or without longitudinal septa, in moderately long to long, simple or branched chains, with dark septa and cell walls. Apically or laterally form secondary conidiophores with one or a few conidiogenous loci. Sometimes produced chlamydospores.
      Sect. ChalastosporaConidiophoresShort to long, simple or branched, with one or several conidiogenous loci.Species in this section are primarily reported as saprobes and causal agents of human diseases.[11,30,38]
      ConidiaPale to medium brown, narrowly ellipsoidal to ellipsoidal or ovoid, beakless, with no or multiple transverse eusepta and rarely longitudinal septa, solitary or in chains. Apically or laterally form secondary conidiophores with one or a few conidiogenous loci.
      Sect. CheiranthusConidiophoresShort to moderately long, simple or branched, with one or several conidiogenous loci.Species in this section are primarily saprobes and pathogens on various plant hosts.[11,38,55]
      ConidiaOvoid, broadly ellipsoid with transverse and longitudinal septa, slightly or strongly constricted at the septa, in short to long, simple or branched chains.
      Sect. CrivelliaConidiophoresStraight or curved, simple or branched, with geniculate, sympodial proliferations.Species in this section are mainly known as pathogens on opium poppy (Papaver somniferum L.), the sexual morph of which links with genus Crivella.[11,58]
      ConidiaCylindrical, straight to curved to inequilateral, with transverse septa, rarely constricted at septa, single or in short, simple or branched chains. Apically or laterally form secondary conidiophores. Sometimes produced microsclerotia or chlamydospores.
      Sect. DianthicolaConidiophoresSimple or branched, with or without apical geniculate proliferations.Species in this section mainly cause leaf spot and blight on economic vegetation hosts such as carnation (Dianthus sp.) and sesame (Sesamum indicum L.).[11,104,105]
      ConidiaNarrowly ovoid or narrowly ellipsoid with transverse and few longitudinal septa, slightly constricted at the septa, with a long (filamentous) beak or apical secondary conidiophore, solitary or in short chains.
      Sect. EmbellisiaConidiophoresSimple, septate, straight or with geniculate sympodial proliferation.Species in this section are reported as pathogens on vegetable crops such as tomato and garlic.[11,106,107]
      ConidiaSolitary, ovoid to subcylindrical, straight to inequilateral, with transverse septa; septa can be thick, dark and rigid in contrast to the external wall. Sometimes sporulated chlamydospores.
      Sect. EmbellisioidesConidiophoresSimple, septate conidiophores, straight or with multiple, geniculate, sympodial proliferations.Species in this section are mainly reported as saprobes in soil and pathogen on plant hosts.[9,108,109]
      ConidiaSolitary or in short chains, obovoid to ellipsoid, with transverse and longitudinal septa, transverse septa can be thick, dark and rigid in contrast to the external wall. Apical or lateral, short secondary conidiophores may occur. Sometimes produced sexual morph and chlamydospores.
      Sect. EurekaConidiophoresSimple, septate conidiophores, straight or with geniculate, sympodial proliferations.Species in this section are reported as pathogens and endophytes that are active in the biotransformation of some secondary metabolites.[11,110,111]
      ConidiaSolitary or in short chains, narrowly ellipsoidal to cylindrical, with transverse and longitudinal septa, slightly constricted at the septa, with a blunt rounded apex. Sometimes form apical or lateral, short secondary conidiophores and sporulated sexual morph and chlamydospores.
      Sect. EuphorbiicolaConidiophoresShort to long, broad, apical and sometimes lateral, secondary conidiophores.Species in this section served as pathogens on economic plants such as Euphorbiicola sp. and Citrus sp. and also produced secondary metabolites.[11,112]
      ConidiaMedium to large-sized, in short to moderately long chains, ovoid, obclavate, disto- and euseptate, with multiple transverse and some longitudinal septa, slightly constricted near some transverse septa, with no or a simple long beak in the terminal conidia.
      Sect. GypsophilaeConidiophoresSimple, or occasionally branched, with one or a few conidiogenous loci.Species in this section occur on the host family Caryophyllaceae.[11,14,38]
      ConidiaSolitary or in short chains, ellipsoid to long ovoid, with multiple transverse and longitudinal septa, conspicuously constricted near some transverse septa. Apically form secondary conidiophores with one or two conidiogenous loci or laterally with a single conidiogenous locus.
      Sect. HelianthiinficientesConidiophoresSimple, or branched, with one or a few conidiogenous loci.Species in this section is well-known as a pathogen on sunflower and cosmos, and also associated with some other species in Asteraceae (i.e., Arctium sp. and Sonchus sp.).[6]
      ConidiaSolitary or in short chains, large, narrowly or broadly ovoid, or ellipsoidal, with several transverse and longitudinal septa, constricted near septa, sometimes non-beaked. Apically form secondary conidiophores, or a few lateral secondary conidiophores, or short to very long filiform beak.
      Sect. InfectoriaeConidiophoresShort to long, simple or branched, with one or several conidiogenous loci.Species in this section are known as saprobes as well as plant and human pathogens.[11,14,38,
      70]
      ConidiaModerately long to long, branched chains, small or moderate sized, obclavate to long ellipsoidal, septate, slightly constricted near some septa, with few longitudinal septa. Apically or laterally formed long geniculate, multi-locus secondary conidiophores, with meristematic growth.
      Sect. JaponicaeConidiophoresShort to long, simple or occasionally branched, with a single conidiogenous locus.Species in this section particularly occur on hosts in Brassicaceae.[11,14]
      ConidiaShort to long ovoid with transverse and longitudinal septa, conspicuously constricted at most of the transverse septa, in short chains. Apically formed secondary conidiophores with single conidiogenous locus.
      Sect. NimbyaConidiophoresSimple, short to form moderately long, sometimes one to a few short to long, geniculate, sympodial metastasis.Species in this section are known as saprobes and plant pathogens. Species in this section produce phytotoxins[11,55,85,
      113,114]
      ConidiaSolitary or in short chains, narrowly elongate-obclavate, gradually tapering apically, with transverse disto- and eusepta, sometimes slightly constricted near eusepta.
      Sect. OmanensesConidiophoresLong, simple, with multiple geniculate, sympodial metastasis or short conidiogenous loci normally with a terminal cluster of three conidia.Species in this section consist of a core taxon A. omanensis which is saprobic on dead woods.[7]
      ConidiaSolitary, obovoid and sphaeroid, non-beaked, with transverse and longitudinal septa.
      Sect. PanaxConidiophoresSimple or branched, short to moderately long, with one or a few conidiogenous loci.Species in this section are known as pathogens causing blight on economic plants such as ginseng and American ginseng (Araliaceae).[11,14,115]
      ConidiaSolitary, simple or branched, in short chains, obclavate to ovoid, with multiple transverse and longitudinal septa, conspicuously constricted near several transverse septa, apically formed secondary conidiophores with one or several conidiogenous loci, multiple lateral secondary conidiophores with a single conidiogenous locus.
      Sect. PhragmosporaeConidiophoresSimple, short to moderately long, with one or multiple geniculate, sympodial metastasis.Species in this section are mainly known as saprobes from soil and marine environments.[11]
      ConidiaSolitary or in simple short chains, broadly ovoid to long ovoid, ellipsoidal, curved, or limaciform, with multiple transverse and few to multiple longitudinal septa, some septa darkened, slightly to conspicuously constricted near several transverse septa, apically formed secondary conidiophores with one or several conidiogenous loci.
      Sect. PorriConidiophoresShort to long, simple, with one or several conidiogenous loci.Species in this section consist of some important phytopathogens and produce phytotoxins.[11,14,22,116,117]
      ConidiaSolitary or in short to moderately long chains, with a simple or branched, long to filamentous beak, medium or large size, broadly ovoid, obclavate, ellipsoid, subcylindrical or obovoid, disto- and eusepta, with multiple transverse and longitudinal septa, slightly constricted near some transverse septa, apically or laterally formed secondary conidiophores.
      Sect. PseudoalternariaConidiophoresSimple or branched, septate, smooth, medium brown, simple with a single apical pore, with short to long, simple to multi-geniculate secondary conidiophores with one to many conidiogenous loci.Species in this section are known as pathogens on plant hosts.[15]
      ConidiaMostly catenulate, ellipsoid to obclavate, medium brown to golden brown, with several transverse and longitudinal septa, smooth, secondary conidiophore may occur as a false beak.
      Sect. PseudoulocladiumConidiophoresSimple or branched, with short, geniculate, sympodial metastasis.Species in this section are reported as phytopathogens for human infection.[11]
      ConidiaObovoid, non-beaked with a narrow base, in simple or mostly branched chains, apically formed secondary conidiophores with multiple conidiogenous loci and laterally secondary conidiophores may occur with a single conidiogenous locus.
      Sect. RadicinaConidiophoresStraight, simple or branched, short or long, with multiple, short geniculate, sympodial proliferations, with one to a few conidiogenous loci at the apex.Species in this section mainly occur on hosts in family Apiaceae.[11]
      ConidiaSolitary or in short chains, moderate in size, broadly ovoid to narrowly ellipsoidal, beakless, with several transverse and longitudinal septa, apically formed solitary, short, secondary conidiophores.
      Sect. SodaConidiophoresSimple or occasionally branched, short to moderately long, with one conidiogenous locus.Species in this section are isolated from soda lake environments (Western Siberia, Russia).[56]
      ConidiaSolitary or in short to long, simple or branched chains, moderate to very large in size, narrowly ellipsoid to elongate-ovoid or somewhat obclavate, septate, with transverse and longitudinal septa, conspicuously constricted at most of the transverse septa, produced microsclerotia or chlamydospores, apical or lateral short secondary conidiophores with a single conidiogenous locus may occur, and conidiogenous tip can be enlarged.
      Sect. SonchiConidiophoresSimple or branched, with short, geniculate, with one or several conidiogenous loci.Species in this section mainly occur on a wide range of hosts within Asteraceae (Compositae).[14]
      ConidiaSingle or in short chains, medium to large size, subcylindrical, broadly ovoid, broadly ellipsoid or obclavate, with multiple transverse and few longitudinal septa, slightly constricted at the septa.
      Sect. TeretisporaConidiophoresSimple, sometimes extending at the apex with one or two, geniculate, sympodial proliferations.Species in this section consist of a core species, Alternaria leucanthemi, which is a phytopathogen causing plant blight disease.[11,38]
      ConidiaSingle, long cylindrical, lacking a beak portion, with many transverse and a few longitudinal septa, constricted at most of the transverse septa, secondary conidiophores with single conidium from the base of primary conidium and rarely formed apically.
      Sect. UlocladioidesConidiophoresShort, geniculate, sympodial proliferations.Species in this section are mainly known as phytopathogens causing leaf spot disease and can be saprobes on a variety of host substrates as well as a causal agent of keratitis.[11,15]
      ConidiaObovoid, non-beaked with a narrow base, single or in chains, with apical secondary conidiophores.
      Sect. UlocladiumConidiophoresSimple, with one or two short, geniculate, sympodial proliferations.Species in this section are mainly isolated from plant litter and rarely from marine environments. Potential bioactivities were also reported.[11,118]
      ConidiaSingle, obovoid, non-beaked, with a narrow base.
      Sect. UndifilumConidiophoresSimple, septate, straight, or with geniculate sympodial proliferation.Species in this section mainly occur on hosts in family Fabaceae.[11]
      ConidiaOvate to obclavate to long ellipsoid, straight to inequilateral, single, transverse septa, septa can be thick, dark and rigid, and form unique germ tubes, which are wavy or undulate until branching.

      Table 1. 

      Synopsis of Alternaria sections based on the asexual morphs.

    • Gene lociPrimersSequence 5’–3’References
      Internal transcribed spacer region (ITS, including the 5.8S gene)ITS5GGA AGT AAA AGT CGT AAC AAG G[139]
      ITS4TCC TCC GCT TAT TGA TAT GC
      28S large subunit rDNA (LSU)LR0RGTA CCC GCT GAA CTT AAG C[140]
      LR5ATC CTG AGG GAA ACT TC
      18S small subunit rDNA (SSU)NS1GTA GTC ATA TGC TTG TCT C[139]
      NS4CTT CCG TCA ATT CCT TTA AG
      Alternaria major allergen (Alt-a1)Alt-forATG CAG TTC ACC ACC ATC GC[49]
      Alt-revACG AGG GTG AYG TAG GCG TC
      Glyceraldehyde 3-phosphate Dehydrogenase (GAPDH)GDP-1CAA CGG CTT CGG TCG CAT TG[141]
      GDP-2GCC AAG CAG TTG GTT GTG C
      Plasma membrane ATPase (ATPase)ATPDF1ATC GTC TCC ATG ACC GAG TTC G[14]
      ATPDR1TCC GAT GGA GTT CAT GAT AGC C
      The second largest subunit of RNA polymerase II (RPB2)fRPB2-5fGAY GAY MGW GAT CAY TTY GG[142]
      fRPB2-7cRCCC ATR GCT TGY TTR CCC AT
      Translation elongation factor 1-α (TEF1-α)EF1-983FGCY CCY GGH CAY CGT GAY TTY AT[143]
      EF1-2218RATG ACA CCR ACR GCR ACR GTY TG
      EF1-728FCATCGAGAAGTTCGAGAAGG[144]
      EF1-986RTACTTGAAGGAACCCTTACC

      Table 2. 

      Gene loci and primers used in this study.

    • Phylogenetic analysesNucleotide substitution models
      ITSLSUSSUGAPDHRPB2TEF1-αAlt-a1ATPase
      A1: Alternaria sectionsGTR+I+GGTR+GTrN+I+GSYM+I+GGTR+I+GTIM1+I+GGTR+I+Gn/a
      A2: A. alternataGTR+I+GGTR+I+GGTR+I+GGTR+I+GTIM2 +GGTR+I+GGTR+I+Gn/a
      A3: sect. InfectoriaeGTR+I+Gn/an/aGTR+I+Gn/an/an/aSYM+G
      A4: sect. PorriSYM+I+Gn/an/aTIM2+I+GGTR+I+GGTR+GGTR+I+Gn/a
      A5: sect. RadicinaGTR+I+Gn/an/aGTR+I+GTIM2+GGTR+I+Gn/an/a

      Table 3. 

      The best nucleotide substitution model for each locus based on the Akaike Information Criterion (AIC) generated by MrModeltest v. 2.3.[156].

    • OrderFamilyGenusSectionsDivergence times (crown age)Divergence times (stem age)
      Pleosporales233 (168–301) Mya252 (184–326) Mya
      Pleosporaceae110 (79–148) Mya120 (84–159) Mya
      Alternaria53 (36–71) Mya62 (42–85) Mya
      Alternaria sect. Alternantherae0.4 (0–1.5) Mya14 (6.7–21) Mya
      Alternaria sect. Alternaria5 (1.7–10) Mya14 (6.7–21) Mya
      Alternaria sect. Brassicicola2.3 (0.5–5.5) Mya33 (22–45) Mya
      Alternaria sect. Chalastospora16 (8.8–26) Mya26 (16–38) Mya
      Alternaria sect. Cheiranthus11 (4.23–20) Mya26 (16–38) Mya
      Alternaria sect. Crivellia7.6 (1.5–19) Mya53 (36–71) Mya
      Alternaria sect. Dianthicola11 (5.4–18) Mya17 (10–27) Mya
      Alternaria sect. Embellisia7.4 (2.5–15) Mya28 (14–43) Mya
      Alternaria sect. Embellisioides11 (5–19) Mya24 (14–36) Mya
      Alternaria sect. Eureka14 (5.6–24) Mya28 (18–44) Mya
      Alternaria sect. Euphorbiicola-11 (5.6–17) Mya
      Alternaria sect. Gypsophilae16 (7.6–26) Mya27 (18–37) Mya
      Alternaria sect. Helianthiinficientes0.11 (0–0.3) Mya24 (13–36) Mya
      Alternaria sect. Infectoriae9.5 (4–17) Mya26 (16–38) Mya
      Alternaria sect. Japonicae31 (14–47) Mya
      Alternaria sect. Nimbya24 (11–39) Mya36 (28–51) Mya
      Alternaria sect. Omanenses30 (14–47) Mya
      Alternaria sect. Panax14 (6.8–23) Mya22 (12–33) Mya
      Alternaria sect. Phragmosporae28 (13–44) Mya42 (28–58) Mya
      Alternaria sect. Porri6.7 (3–11) Mya11 (5.6–17) Mya
      Alternaria sect. Pseudoalternata28 (14–43) Mya*
      Alternaria sect. Pseudoulocladium2.1 (0.4–5.8) Mya17 (9.5–27) Mya
      Alternaria sect. Radicina9.3 (3.6–18) Mya29 (19–40) Mya
      Alternaria sect. Soda3 (0.5–8.4) Mya32 (26–54) Mya
      Alternaria sect. Sonchi6.8 (2–14) Mya24 (13–36) Mya
      Alternaria sect. Teretispora0.2 (0–1.03) Mya27 (17–40) Mya
      Alternaria sect. Ulocladioides8.1 (3–17) Mya22 (13–32) Mya
      Alternaria sect. Ulocladium0.9 (0.1–2.5) Mya44 (32–60) Mya
      Alternaria sect. Undifilum45 (32–62) Mya

      Table 4. 

      Divergence times of Alternaria sections indicated in MCC tree. The age value with '*' indicates recent results lacking key coding gene strains.

    • Culture collectionOriginal
      code
      Herbarium no.OriginHost and habitatCollection dateCollector
      KUNCC 22-10823IT2053HKAS 124866
      MFLU 15-2585
      Italy, Province of Forlì-Cesena, PremilcuoreDead stem of Sonchus sp. (Asteraceae)18 August 2014E. Camporesi
      KUNCC 22-10824IT2063HKAS 124867Italy, Province of Forlì-Cesena, Verghereto, MontecoronaroDead hanging stem of Centaurea sp. (Asteraceae)20 August 2014E. Camporesi
      KUNCC 22-10825IT2064HKAS 124868Italy, Province of Forlì-Cesena, Fiumicello di PremilcuoreDead hanging stem of Helleborus sp. (Ranunculaceae).28 August 2014E. Camporesi
      KUNCC 22-10826IT2087HKAS 124869Italy, Province of Forlì-Cesena, Quattro di ForlìDead hanging stem of Agropyron sp. (Asteraceae)1 September 2014E. Camporesi
      KUNCC 22-10827IT2090HKAS 124870Italy, Province of Forlì-Cesena, Predappio, Rocca delle CaminateDead leaf petiole of Robinia sp. (Fabaceae)4 September 2014E. Camporesi
      KUNCC 22-10828IT2103HKAS 124871Italy, Province of Forlì-Cesena, MeldolaDead hanging stem of Echinochloa
      sp. (Poaceae)
      8 September 2014E. Camporesi
      KUNCC 22-10829IT2114HKAS 124872Italy, Province of Forlì-Cesena, TesselloDead hanging stem of Cephalaria sp. (Dipsacaseae)16 September 2014E. Camporesi
      KUNCC 22-10830IT2115HKAS 124873Italy, Province of Forlì-Cesena, Civitella di RomagnaDead hanging stem of Aster sp. (Asteraceae)19 September 2014E. Camporesi
      KUNCC 22-10831IT2125HKAS 124874Italy, Province of Arezzo, Stia, MontemezzanoDead hanging stem of Euphorbia sp. (Euphorbiaceae)22 September 2014E. Camporesi
      KUNCC 22-10832IT2143HKAS 124875Italy, Province of Forlì-Cesena, Galeata, San ZenoDead hanging leaf petiole of
      Ailanthus sp. (Simaroubaceae)
      30 September 2014E. Camporesi
      KUNCC 22-10833IT2144HKAS 124876Italy, Province of Forlì-Cesena,
      Cabelli di Santa Sofia
      Dead hanging stem of Agrostis sp. (Poaceae)2 October 2014E. Camporesi
      KUNCC 22-10834IT2145HKAS 124877Italy, Province of Forlì-Cesena,
      Monte Mirabello
      Dead hanging leaf of Arundo sp. (Poaceae)3 October 2014E. Camporesi
      KUNCC 22-10835IT2162HKAS 124878Italy, Province of Forlì-Cesena,
      Santa Sofia
      Dead hanging stem of Hedysarum coronarium L. (Papilionaceae)7 October 2014E. Camporesi
      KUNCC 22-10836IT2166HKAS 124879Italy, Province of Forlì-Cesena, Meldola, PiandispinoDead hanging stem of Dipsacus sp. (Caprifoliaceae)7 October 2014E. Camporesi
      KUNCC 22-10837IT2277HKAS 124880Italy, Province of Ravenna, Lido di DanteDead hanging stem of Kali tragus (L.) Scop. (Amaranthaceae)2 December 2014E. Camporesi
      KUNCC 22-10838IT2347HKAS 124881Italy, Province of Forlì-Cesena,
      Collina di Forlì
      Several samaras of Fraxinus oxycarpa Willd. (Oleaceae)21 January 2015E. Camporesi
      KUNCC 22-10839IT2427MFLU 15-1823Italy, Province of Forlì-Cesena, Forlì, Via NenniDead hanging stem of Wisteria sp. (Caprifoliaceae)30 March 2015E. Camporesi
      KUNCC 22-10840IT2454HKAS 124883Italy, Province of Forlì-Cesena, Predappio, Rocca delle CaminateDead stem of Urtica sp. (Urticaceae)21 April 2015E. Camporesi
      KUNCC 22-10841IT2900MFLU 16-1116Italy, Province of Forlì-Cesena, Santa Sofia, CamposonaldoDead needles of Pinus nigra
      J.F. Arnold (Pinaceae)
      23 March 2016E. Camporesi
      KUNCC 22-10842IT3048MFLU 16-2277Italy, Province of Forlì-Cesena, Fiumicello di PremilcuoreDead hanging stem of Acer opalus Mill. (Sapindaceae)27 July 2016E. Camporesi
      KUNCC 22-10843IT3160MFLU 16-2883Italy, Province of Forlì-Cesena, Forlì, Ravaldino in MonteDead stem of Silybum marianum (L.) Gaertn. (Asteraceae)15 November 2016E. Camporesi
      KUNCC 22-10844IT3168MFLU 16-2904Italy, Province of Forlì-Cesena, Forlì, Parco UrbanoDead hanging fruits of Ostrya carpinifolia Scop. (Betulaceae)19 November 2016E. Camporesi
      KUNCC 22-10845IT3419HKAS 124888Italy, Province of Arezzo, Poppi, QuotaDead hanging stem of Calamintha nepeta (Lamiaceae)25 July 2017E. Camporesi
      KUNCC 22-10846IT3426HKAS 124889Italy, Province of Arezzo, near Croce di PratomagnoDead hanging stem of Malva alcea L. (Malavaceae)1 August 2017E. Camporesi
      KUNCC 22-10847IT3439HKAS 124890Italy, Province of Arezzo, Stia, MontemezzanoDead hanging stem of Reseda luteola L. (Resedaceae)13 August 2017E. Camporesi
      KUNCC 22-10848IT3442HKAS 124891Italy, Province of Arezzo, MontemignaioDead hanging stem of Valeriana sp. (Caprifoliaceae)12 August 2017E. Camporesi
      KUNCC 22-10849IT3449HKAS 124892Italy, Province of Forlì-Cesena, Bagno di Romagna, RiofreddoDead hanging stem of Tanacetum
      sp. (Asteraceae)
      22 August 2017E. Camporesi
      KUNCC 22-1050IT3504MFLU 17-1778Italy, Province of Forlì-Cesena, Bagno di Romagna, AcquapartitaDead hanging stem of Orobanche
      sp. (Orobanchaceae)
      25 September 2017E. Camporesi
      KUNCC 22-10851IT3556HKAS 124894Italy, Province of Forlì-Cesena, Santa SofiaDead leaf of Sorbus aria Crantz (Rosaceae)15 November 2017E. Camporesi
      KUNCC 22-10852IT3598HKAS 124895Italy, Province of Ravenna, Faenza, Santa LuciaDead leaves of Quercus pubescens Willd. (Fagaceae)13 December 2017E. Camporesi
      KUNCC 22-10853IT3651HKAS 124896Italy, Province of Forlì-Cesena, MeldolaDead hanging branch of Sambucus nigra L. (Adoxaceae)31 December 2017E. Camporesi
      KUNCC 22-10854KIB-H2HKAS 124897China, Yunnan, Kunming Institute of BotanyDead fallen leave of bamboo (Poaceae)26 December 2014J.F. Li
      KUNCC 22-10855HKM-1HKAS 124898China, Yunnan, Kunming, XundianDead stem of Raphanus sativus L. (Brassicaceae)13 March 2015J.F. Li
      KUNCC 22-10856H-49HKAS 124899China, Yunnan, BaoshanDead branch of Capsicum annuum L. (Solanaceae)22 October 2015J.F. Li
      KUNCC 22-10857PB-12HKAS 124900China, Yunnan, Pingbian, Dawei MountainDead stem of Zea mays L. (Poaceae)20 September 2017J.F. Li
      KUNCC 22-10858HXB-08HKAS 124901China, Yunnan, XishuangbannaDead fallen leaves of Dimocarpus longan Lour. (Sapindaceae)8 June 2018, J.F. Li
      KUNCC 22-10859HAM-02HKAS 124902China, Yunnan, Honghe, Amu MountainDead fallen leaves of grass (Poaceae)15 June 2018J.F. Li
      KUNCC 22-10860HAM-03HKAS 124903China, Yunnan, Honghe, Amu MountainDead aerial stem of Capsicum
      annuum
      (Solanaceae)
      15 June 2018J.F. Li
      KUNCC 22-10861HSH-01HKAS 124904Thailand, Chiang Rai, Muang, Singha ParkDead culms of bamboo (Poaceae)23 February 2016J.F. Li
      KUNCC 22-10862HMRC-51HKAS 124905Thailand, Chiang Mai, Mae Taeng, Mushroom Research Center (M.R.C)Dead fallen leaves of unidentified plant23 March 2016J.F. Li
      KUNCC 22-10863DMS-15HKAS 124906Thailand, Chiang Rai, Doi Mae SalongDead leaves of grass (Poaceae)24 May 2016J.F. Li
      KUNCC 22-10864HTWD-01HKAS 124807Thailand, Chiang Rai, Mae Fah LuangDead leaves of palm (Arecaceae)25 September 2016J.F. Li
      KUNCC 22-10865H-71HKAS 124908Thailand, Chiang Rai, Doi ChangDead leaves of Coffea arabica L. (Rubiaceae)25 July 2018J.F. Li
      KUNCC 22-10866HWP-01HKAS 124909Thailand, Chiang Rai, Wiang Pa PaoDead stems of Bidens pilosa L. (Asteraceae)16 October 2018J.F. Li

      Table 5. 

      Additional collections of Alternaria alternata collected from Yunnan, China, Italy and Thailand in this study.

    • Species nameStrain no.Nucleotide difference of gene sequences (no gaps)
      A. doliconidiumMFLUCC 14-0020ITSTEF1-αRBP2GAPDHAlt-a1
      A. alternataCBS 1025958/520 bp (1.5%)14/256 bp (4.7%)30/875 bp (3.4%)16/582 bp (2.7%)12/476 bp (2.5%)
      A. alternataCBS 916.968/520 bp (1.5%)14/256 bp (4.7%)28/875 bp (3.2%)18/582 bp (3.1%)12/476 bp (2.5%)
      A. alternataCBS 175.5210/520 bp (1.9%)16/256 bp (6.3%)30/875 bp (3.4%)17/582 bp (2.9%)12/476 bp (2.5%)
      A. alternataYL19/520 bp (1.7%)14/256 bp (4.7%)30/875 bp (3.4%)16/582 bp (2.7%)12/476 bp (2.5%)
      A. alternataYL29/520 bp (1.7%)14/256 bp (4.7%)30/875 bp (3.4%)17/582 bp (2.9%)12/476 bp (2.5%)
      A. doliconidiumHKAS 1008401/520 bp, (0.2%)0%N/AN/AN/A
      A. doliconidiumMFLUCC 17-02631/520 bp, (0.2%)0%N/AN/AN/A
      A. italicaMFLUCC 14-02316/520 bp, (1.2%)11/256 bp (4.3%)25/875 bp, (2.9%)N/AN/A
      A. italicaKUMCC 17-01237/520 bp, (1.3%)N/AN/AN/AN/A

      Table 6. 

      Nucleotide base comparison of Alternaria doliconidium (MFLUCC 14-0020) with closely related taxa.