The subclasses There are seven subclasses accepted in Sordariomycetes with the addition of Pisorisporiomycetidae in this paper.
Diaporthomycetidae Senan., Maharachch. & K.D. Hyde, Fungal Divers. 72: 208 (2015) The subclass Diaporthomycetidae was introduced by Maharachchikumbura et al. (2015) for some taxa already placed in Sordariomycetidae, but that were phylogenetically and morphologically distinct from Sordariomycetidae. Members of Diaporthomycetidae occur in both aquatic and terrestrial habitats as saprobes, pathogens, or endophytes. Previously there were ten orders in this subclass (Hongsanan et al. 2017). Crous et al. (2017a) introduced Pararamichloridiales and Crous et al. (2019a) introduced Sporidesmiales. Hyde et al. (2017a) proposed Catabotryales based on evolutionary data and here we formally introduce it. Currently there are 15 orders and 65 families in this subclass (Hyde et al. 2017a, this paper). The divergence time for Diaporthomycetidae is estimated as 247 MYA (Fig. 2). The orders and families in this subclass are mostly well-supported in our phylogenetic analysis (Figs 6, 8, 13, 14, 18).
Hypocreomycetidae O.E. Erikss. & Winka, Myconet 1(1): 6 (1997) Maharachchikumbura et al. (2016b) accepted Conioscyphales, Coronophorales, Falcocladiales, Glomerellales, Hypocreales, Melanosporales, Microascales, Pleurotheciales and Savoryellales in Hypocreomycetidae. Yang et al. (2016b) introduced Fuscosporellales to the subclass based on LSU, SSU and rpb2 sequence data. Hongsanan et al. (2017) placed Fuscosporellales and Pleurotheciales in the newly introduced subclass Savoryellomycetidae. The families Etheirophoraceae, Juncigenaceae and Torpedosporaceae have previously been treated in Torpedosporales by Jones et al. (2015), but Torpedosporales was maintained in Hypocreomycetidae, incertae sedis by Maharachchikumbura et al. (2015). Maharachchikumbura et al. (2016b) accepted Torpedosporales in Hypocreomycetidae and this was confirmed by Hongsanan et al. (2017) based on the divergent time estimates. Later, Parasympodiellales was added to the subclass by Hernández-Restrepo et al. (2017). Our phylogenetic analysis of a combined LSU, SSU, tef1, rpb2 sequence data (Figs. 1, 24) also supports the placement of Torpedosporales in Hypocreomycetidae. Currently there are seven orders (Coronophorales, Falcocladiales, Glomerellales, Hypocreales, Microascales, Parasympodiellales and Torpedosporales) and 37 families in this subclass (Hyde et al. 2017a, this paper). The divergence time for Hypocreomycetidae has been estimated as 256.5 MYA (Fig. 2). The orders in this subclass are mostly well-supported in our analysis, except Torpedosporales (Fig. 1).
Lulworthiomycetidae Dayar., E.B.G. Jones & K.D. Hyde, Fungal Divers. 72: 208 (2015) Maharachchkumbura et al. (2016b) established the subclass Lulworthiomycetidae to accommodate Koralionastetales, Lulworthiales and Pisorisporiales as proposed by Maharachchikumbura et al. (2015). Taxa related to Lulworthiomycetidae are saprobic on wood, sea grasses and marsh plants or parasites on algae. The divergence time for Lulworthiomycetidae has been estimated as 257 MYA (Fig. 2). Currently there are two orders and two families in this subclass and Pisorisporiales is transferred to the introduced subclass Pisorisporiomycetidae in this study.
Pisorisporiomycetidae Bundhun, Maharachch. & K.D. Hyde, subclass nov. Index Fungorum number: IF556880; Facesoffungi number: FoF06688 Saprobic on submerged wood or driftwood. Sexual morph: Ascomata astromatic, perithecial, solitary or aggregated in small groups, immersed, semi-immersed to superficial, ostiolate. Ostiole periphysate. Peridium 2-layered, leathery to fragile, partly carbonaceous. Paraphyses abundant,-
Figure 1 – Maximum likelihood (ML) majority rule combined LSU, SSU, tef1 and rpb2 consensus tree for the analyzed Sordariomycetes isolates. Families are indicated in yellow and green coloured blocks and orders are indicated in dark and light grey coloured blocks. RAxML bootstrap support values (MLB above 50 %) are given at the nodes. The scale bar represents the expected number of changes per site. The tree is rooted with Botryotinia fuckeliana (AFTOL ID-59), Dothidea sambuci (DAOM 231303), and Pyxidiophora arvernensis (AFTOL-ID 2197).
Figure 1 – Continued.
Figure 1 – Continued.
-hyaline, persistent. Asci 8-spored, unitunicate, pedicellate, persistent, with a J+ or J-, apical ring. Ascospores hyaline, multi-septate, often guttulate, lacking any mucilaginous sheath or appendages. Asexual morph: Undetermined. Type order – Pisorisporiales Réblová & J. Fourn. Notes – Pisorisporiales was reported to form a sister clade with Lulworthiales and Koralionastetales in Lulworthiomycetidae with a stem age of 266 MYA (Hongsanan et al. 2017, Hyde et al. 2017a). This is congruent to the results obtained in the present study (257 MYA). Since this stem age falls within the subclass status range (250–300 MYA), Pisorisporiomycetidae is proposed here as a new subclass. This subclass contains Pisorisporiales, family Pisorisporiaceae and the two genera Achroceratosphaeria and Pisorisporium (Réblová et al. 2015a).
Figure 1 – Continued.
Divergence times of lineages were used to analyze the status of higher ranks of fungi (Hongsanan et al. 2017, 2018, Hyde et al. 2017, Liu et al. 2017). Hyde et al. (2017) provided a maximum clade credibility (MCC) tree of families in Sordariomycetes and also proposed a series of evolutionary periods that could be used as a guide to define ranking of fungi in Sordariomycetes. In our paper, we provide the MCC tree base on updated classification of Sordariomycetes (Fig. 2). The same dataset as in Fig. 1 was used in our molecular clock analysis to compare the phylogenetic placement generated from both approaches. We use divergence time to confirm familial status of families in Sordariomycetes according to the guidance of Hyde et al. (2017). Some families and orders are not supported by divergence times, but their status is retained due to their unique characters or lack of species (notes are provided in each family).
Figure 2 – The maximum clade credibility (MCC) tree, using the same dataset from Fig. 1. This analysis was performed in BEAST v1.10.2. The crown age of Sordariomycetes was set with Normal distribution, mean = 250, SD = 30, with 97.5% of CI = 308.8 MYA, and crown age of Dothideomycetes with Normal distribution mean = 360, SD = 20, with 97.5% of CI = 399 MYA. The substitution models were selected based on jModeltest2.1.1; GTR+I+G for LSU, rpb2 and SSU, and TrN+I+G for tef1 (the model TrN is not available in BEAUti 1.10.2, thus we used TN93). Lognormal distribution of rates was used during the analyses with uncorrelated relaxed clock model. The Yule process tree prior was used to model the speciation of nodes in the topology with a randomly generated starting tree. The analyses were performed for 100 million generations, with sampling parameters every 10000 generations. The effective sample sizes were checked in Tracer v.1.6 and the acceptable values are higher than 200. The first 20% representing the burn-in phase were discarded and the remaining trees were combined in LogCombiner 1.10.2., summarized data and estimated in TreeAnnotator 1.10.2. Bars correspond to the 95% highest posterior density (HPD) intervals. The scale axis shows divergence times as millions of years ago (MYA).
Figure 2 – Continued.
Figure 2 – Continued.
Savoryellomycetidae Hongsanan, K.D. Hyde & Maharachch., Fungal Divers. 84: 35 (2017) According to Maharachchikumbura et al. (2016b) and Yang et al. (2016b) Conioscyphales was assigned to Diaporthomycetidae, genera incertae sedis, while Fuscosporellales, Pleurotheciales, and Savoryellales were included in the subclass Hypocreomycetidae. In the phylogenetic and molecular clock analyses of (Hongsanan et al. 2017, Hyde et al. 2017a), Conioscyphales, Fuscosporellales, Pleurotheciales, and Savoryellales clustered together as a distinct clade, with a stem age of 268 MYA. Hence, they were referred to a new subclass Savoryellomycetidae by Hongsanan et al. (2017) and this was reinforced in the paper by Dayarathne et al. (2019a). Our phylogenetic analyses with combined LSU, SSU, ITS and rpb2 sequence data also showed Conioscyphales, Fuscosporellales, Pleurotheciales, and Savoryellales formed well-supported distinct clades (100% ML, 1.00 PP, 100% ML, 1.00 PP, 98% ML, 1.00 PP and 100% ML, 1.00 PP, respectively) within the subclass Savoryellomycetidae (Fig. 10). Currently there are four orders and four families in this subclass (this paper).
Sordariomycetidae O.E. Erikss. & Winka, Myconet 1(1): 10 (1997) The subclass Sordariomycetidae was established by Eriksson & Winka (1997) and comprised six orders, 12 families and two families incertae sedis. Members of this subclass are mainly characterized by dark ascomata with inoperculate, unitunicate asci and occur in terrestrial, aquatic and marine habitats and are widely distributed as plant and animal pathogens, endophytes, saprobes as well as coprophilous and lichenicolous taxa (Maharachchikumbura et al. 2015, 2016b, Huang et al. 2019). They are mycophilic, rich in coprophilous taxa and associated with invertebrates and their ecological aspects and biotechnological potential have been researched (Zhang et al. 2006, Raghukumar 2008, Bovio et al. 2018). An MCC tree based on a combined SSU, LSU, tef1 and rpb2 sequence data revealed that this subclass evolved around 145–216 MYA (Hongsanan et al. 2017, Hyde et al. 2017a). The divergence time for Sordariomycetidae is estimated as 247 MYA (Fig. 2). Currently there are eight orders and 19 families in this subclass (this paper).
Xylariomycetidae O.E. Erikss & Winka, Myconet 1: 12 (1997) Different outlines of Xylariomycetidae have been published by Maharachchikumbura et al. (2016b), Samarakoon et al. (2016b) and Hongsanan et al. (2017). However, in the present study, we have revised the subclass. Concatenated LSU, ITS, rpb2 and tub2 based maximum likelihood phylogeny resulted in a well-supported backbone tree for 34 families in Xylariomycetidae (Fig. 4). The divergence time for Xylariomycetidae is estimated as 278 MYA (Fig. 2). There are three distinct clades in the tree representing the orders discussed in previous studies: Xylariales, Amphisphaeriales and Delonicicolales. The sister orders Xylariales (15 families) and Amphisphaeriales (17 families) have moderate statistical support (55% ML) and basal to these is the highly supported clade Delonicicolales (100% ML). Samarakoon et al. (2016b) and Hongsanan et al. (2017) provided divergence time estimations as additional information for Amphisphaeriales, which is estimated to have diverged from Xylariales around 152–187 Mya and provides evidence for these as distinct orders. Families accepted in Amphisphaeriales in this paper are similar to Hongsanan et al. (2017). In this study, we accept Cainiaceae as placed in Xylariales (Figs 1, 4), while Iodosphaeriaceae (Figs 1, 4) which was previously referred to the Xylariomycetidae incertae sedis, (Hongsanan et al. 2017) is placed in Amphisphaeriales. Xyladictyochaetaceae (Crous et al. 2018b) is accepted in Amphisphaeriales and clusters with Phlogicylindriaceae with high statistical support (95% ML; Fig. 4). Hansfordiaceae (Crous et al. 2019b) is sister to Coniocessiaceae in Xylariales with strong statistical support (82% ML; Fig. 4). Cylindriaceae (Crous et al. 2018b) and Pseudotruncatellaceae (Crous et al. 2019b) are placed in Amphisphaeriales with poor statistical support (Fig. 4). Induratiaceae will be introduced by Samarakoon et al. (2020) and is placed in Xylariales (Fig. 4). Voglmayr et al. (2019a) introduced Leptosilliaceae as a new family which is sister to Delonicicolaceae, while rejecting Delonicicolales. However, with high statistical support (Fig. 4), we accept Delonicicolales in this study. Currently there are three orders and 35 families in this subclass (this paper).
Figure 3 – Phylogram generated from maximum likelihood analysis based on combined LSU, SSU, ITS and rpb2 sequence data of Diaporthomycetidae. One hundred and ninety-three strains are included in the combined analyses which comprised 3545 characters (859 characters for LSU, 972 characters for SSU, 659 characters for ITS) after alignment. Single gene analyses were carried out and the topology of each tree had clade stability. Tree topology of the maximum likelihood analysis is similar to the Bayesian analysis. The best RaxML tree with a final likelihood value of 68207.368884 is presented. Estimated base frequencies were as follows: A = 0.248206, C = 0.241993, G = 0.285500, T = 0.224301; substitution rates AC = 1.369088, AG = 2.887040, AT = 1.413053, CG = 1.152137, CT = 6.303994, GT = 1.000000; gamma distribution shape parameter a = 0.315782. Bootstrap support values for ML greater than 75% and Bayesian posterior probabilities greater than 0.95 are given near the nodes. The tree is rooted with Diatrype disciformis (AFTOL-ID 927). Ex-type strains are in bold. The newly generated sequences are indicated in blue.
Figure 3 – Continued.
Figure 3 – Continued.