Research Article
Print
Research Article
The taxonomy of the model filamentous fungus Podospora anserina
expand article infoS. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud§, Robert Debuchy|, Sven J. Saupe, Alfons J. M. Debets#, Eric Bastiaans#, Fabienne Malagnac|, Pierre Grognet|, Leonardo Peraza-Reyes¤, Pierre Gladieux«, Åsa Kruys», Philippe Silar˄, Sabine M. Huhndorf˅, Andrew N. Miller¦, Aaron A. Vogan»
‡ Uppsala Univeristy, Uppsala, Sweden
§ Université Paris-Saclay, Orsay, France
| Université Paris-Saclay, Gif-sur-Yvette, France
¶ Université de Bordeaux, Bordeaux, France
# Wageningen University, Wageningen, Netherlands
¤ Universidad Nacional Autónoma de México, Mexico City, Mexico
« Université de Montpellier, Montpellier, France
» Uppsala University, Uppsala, Sweden
˄ Université de Paris, Paris, France
˅ The Field Museum, Chicago, United States of America
¦ University of Illinois, Champaign, United States of America
Open Access

Abstract

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Keywords

phylogenetics, Podospora, Podosporaceae, taxonomy

Introduction

Podospora anserina is a model filamentous fungus that has been at the forefront of molecular biology and genetics for over 100 years (Silar 2020). It has been instrumental in numerous important biological breakthroughs, such as the discovery of eukaryotic plasmids and prions and has been monumental in furthering the fields surrounding aging/senescence, meiotic drive, allorecognition (known as heterokaryon incompatibility in fungi), sexual reproduction and genome defence (Esser 1974; Saupe et al. 2000; Saupe 2007; Silar 2013, 2020; Grognet et al. 2019; Vogan et al. 2019). Along with its role in basic research, P. anserina has also caught the attention of industry, where it is used as a source of enzymes that play various roles in the degradation of plant material (Couturier et al. 2016). More recently, P. anserina has burst into the genomics era with one of the first published fungal genomes (Fitzpatrick et al. 2006), released in 2008 (Espagne et al. 2008). In the last year, 10 additional chromosome level assemblies of P. anserina have been released in concert with the genome of the closely-related species, P. comata and P. pauciseta (Silar et al. 2019; Vogan et al. 2019). Future projects will expand on this role even further. Wageningen University hosts a collection of strains isolated from the same locale, spanning 30 years of sampling (van der Gaag et al. 1998, 2000; Vogan et al. 2020), which have now all been sequenced and chromosome level assemblies (in preparation) have been produced for the remaining four species of the Podospora anserina species complex (Boucher et al. 2017). Therefore, the role of P. anserina will continue to be central to many fields in biology and, indeed, likely see use in new fields as new data become public.

The taxonomic history of Podospora anserina has been a long and complex one (reviewed in Silar 2020). Podospora is a member of the Sordariales and has been traditionally grouped within the family Lasiosphaeriaceae, which itself is an artificial assemblage of genera whose main diagnostic is that they do not belong to the Sordariaceae (Lundqvist 1972). Species within the Lasiosphaeriaceae were divided into genera, based primarily on ascospore morphology, but molecular phylogenies have revealed that these characters do not represent synapomorphies and that most of the genera are polyphyletic (Huhndorf et al. 2004; Miller and Huhndorf 2005). A broad phylogenetic treatment of coprophilous Lasiosphaeriaceae defined four separate clades, with species of Podospora represented in all clades, exemplifying the lack of informative morphology amongst these fungi (Kruys et al. 2015). Moreover, the taxon P. anserina itself has survived multiple attempts to rename it in the past, which were unsuccessful in part due to how deeply ingrained the name is in the genetics and molecular biology research community (Boucher et al. 2017; Silar 2020). Recently, this taxonomic mess was stumbled upon by researchers attempting to clean up the distantly-related genus Thielavia (Wang et al. 2019). The authors defined the clade containing the type species of Podospora (P. fimiseda, incorrectly referred to as P. fimicola in Wang et al. 2019) as the Podosporaceae (formerly Lasiosphaeriaceae IV) based on a four-marker phylogeny and further divided this clade into three genera: Podospora, Triangularia and Cladorrhinum. As their analyses suggested that P. anserina is more closely related to the type species of Triangularia (T. bambusae), they proposed the new combination, Triangularia anserina (Wang et al. 2019).

It is the opinion of the authors here that the taxonomic change of P. anserina is both premature and against the ideals of the International Code of Nomenclature for algae, fungi and plants (ICN), as stated in the preamble (Turland et al. 2018). Foremost, it is unlikely that T. anserina will be adopted by many of the researchers that rely on it as a model organism, leading to instability of the name. Furthermore, the phylogeny upon which the change was based has a sparse sampling of the diversity of the family and used only four markers. Here, we demonstrate that there is a lack of information amongst the markers currently sequenced in this group and argue that more data are needed before formal taxonomic changes are made for Podospora. Ultimately, the best solution for taxonomic stability in the Podosporaceae will be to change the type species of Podospora from P. fimiseda, which was conserved in 1972 (Nicolson et al. 1984), to P. anserina and to only define new genera once more sequence data are available, likely in the form of whole genome sequences.

Methods

Sequences and strains

We generated sequences of 29 strains from 27 species in the Podosporaceae family for markers typically used in molecular phylogenetic studies of Sordariomycetes (including Wang et al. 2019): the ribosomal large subunit (LSU), beta-tubulin (Btub) and RNA polymerase II (rpb2) (Table 1). Sequences were generated as per Huhndorf et al. 2004 and Miller and Hundorf 2005. In brief, DNA was extracted from dried ascomata or multispore isolates of growing cultures using a DNeasy Mini Plant extraction kit (Qiagen Inc., Valencia, California), following manufacturer’s recommendations with the exception that tissues were ground in 100 ml AP1 buffer rather than liquid nitrogen. Markers were amplified with the primers listed in Suppl. material 4: Table S1 and sequenced on an Applied Biosystems 3100 automated DNA sequencer. Sequences were deposited in GenBank with accession numbers MT731502MT731583. In addition, we collected available sequences from GenBank and the NBRC culture collection for all strains suspected to fall within the Podosporaceae for the above markers, as well as the fungal barcode ITS (Schoch et al. 2012). For Btub, two regions are often used in phylogenetic analyses. We sequenced the C-terminal domain of Btub with only a single intron (Btub2), but included sequences from databases that correspond to the upstream intron-rich GTPase domain (Btub1) to maximise the number of taxa. When available sequences of markers overlapped with ones that were generated for this study exactly, but had longer flanks, those sequences were merged (two GenBank codes in Table 1). Finally, we included representative strains of the type species of the other families within the Sordariales, as well as the type species of Zopfiella and Cercophora, which have many representatives within the Podosporaceae, as outgroups. The alignment of all concatenated markers is deposited in TreeBase (http://purl.org/phylo/treebase/phylows/study/TB2:S26777).

Table 1.

Strains and markers included in this study. Sequences generated in this study are in bold.

Strain Species Clade ITS LSU BTub1 BTub2 RPB2
CBS 539.89T Apiosordaria backusii A MK926866 MT731508 MK926966 MT731549 MT731570
CBS 106.77 Apiosordaria backusii A MK926867 AY780051 MK926967 AY780085 AY780149
CBS 304.81T Apiosordaria effusa A 3086201b 3086201b
CBS 390.84T Apiosordaria longicaudata A 954801b MT731505 MT731544 MT731580
CBS 244.71T Apiosordaria stercoraria A MH860096 968201b
CBS 629.82T Apiosordaria tenuilacunata A MH861532 MT731507 MT731548 MT731569
CBS 363.84T Apiosordaria tetraspora A MT731506 MT731545 MT731581
NBRC 30422 Apiosordaria verruculosaa A 3042201b 3042201b
NBRC 30423 Apiosordaria verruculosaa A 3042301b 3042301b
CBS 148.77 Apiosordaria verruculosaa A MK926874 MT731510 MK926974 MT731546 MT731577
F-152365 Apiosordaria verruculosaa A AY346258 AY780086 AY780150
CBS 550.66 Apiosordaria verruculosaa A MT731511 MT731547 MT731579
CBS 432.64 Apiosordaria verruculosaa A MH858479 MH870111
CBS 433.64 Apiosordaria verruculosaa A MH858480 MH870112
CBS 268.67 Apiosordaria verruculosaa A MH858965
NBRC 31170T Apiosordaria yaeyamensis A LC146720 LC146720
CBS 120.289 Arnium arizonense A KU955584 KF557671 MT731535 MT731563
S 18211-c Arnium arizonense A KF557668 KF557706
UPS 724 Arnium arizonense A KF557669 KF557707
E00204509 Arnium arizonense A KF557670 KF557708
CBS 307.81T Cercophora samala A MH861345 MH873104
CBS 109.93 Cercophora samala A AY999134 AY999111 AY999140
CBS 125293T Cercophora squamulosa A MH863506
JF 06314T Cercophora aquatica A JN673038 JN673038
SMH 3431 Cercophora striata A AY780065 AY780108 AY780169
SMH 4036 Cercophora striata A KX348038 AY780066
CBS 290.75T Cladorrhinum microsclerotigenum A FN662475 FN662476
CBS 301.90T Cladorrhinum phialophoroides A FM955444 FR692344 KT291718/MK926971 MK876833
ST Podospora anserina A Genomic Genomic Genomic Genomic Genomic
CBS 455.64 Podospora anserina A MT731521 MT731540 MT731564
CBS 533.73 Podospora austroamericana A MT731509 MT731539 MT731582
CBS 724.68T Podospora austroamericana A MK926865 AY999101 MK926965 MK876827
CBS 405.72 Podospora platensis A MH860505 MT731514 MT731550 MT731571
CBS 251.71T Podospora praecox A MH860101 MH871877
FMR 12787 Podospora setosa A KP981441 KP981569 KP981624
CBS 435.50 Podospora setosa A GQ922533 MH868219
CBS 311.58 Podospora setosa A MK926872 MK926872 MK926972 MK876834
CBS 369.59 Podospora setosa A MK926873 MT731515 MK926973 MT731551 MT731572
CBS 265.70 Podospora tarvisina A MH859600 MT731516 MT731552 MT731573
CBS 313.58T Podospora unicaudata A MH857799 MT731513 MT731554 MT731575
CBS 240.71 Podospora unicaudata A MH860093 MH871871
CBS 165.74 Triangularia angulispora A MT731517 MT731543 MT731568
NBRC 30009 Triangularia bambusae a A 3000901b 3000901b
CBS 352.33T Triangularia bambusae a A MK926868 MT731518 MK926968 MT731541 MT731578/MK876830
CBS 381.68T Triangularia batistae A MH859162 MT731519 MT731542 MT731576
IFO 30296 Zopfiella longicaudata A AY999131 AY999109
FMR 12365 Zopfiella longicaudata A KP981448 KP981574 KP981631
FMR 12782 Zopfiella longicaudata A KP981449 KP981575 KP981632
CBS 252.57T Zopfiella longicaudata A MK926869 MT731503 MK926969 MT731536 MT731567
CBS 256.71 Zopfiella longicaudata A MH860106 MH871881
CBS 257.78 Zopfiella longicaudata A MT731504 MT731537 MT731565
CBS 971.73 Zopfiella longicaudata A MT731502 MT731538 MT731566
CBS 671.82T Zopfiella ovina A MH861539 MT731512 MT731553 MT731574
CBS 127120 Zopfiella sp. A MH864427 MH875865
IFO 32904 Zopfiella tetraspora A AY999130 AY999108 AY999139
CBS 245.71 Zopfiella tetraspora A MH860097 MT731520 MT731583
CBS 120012 Arnium olerum a B MT731522 KF557718 MT731561
SMH3253 Arnium olerum a B KF557690
FMR 13412 Arnium sp. B KP981428 KP981555 KP981610
S Arnium tomentosum B KF557691 KF557720
SMH 4089 Cercophora coprophila B KF557692
IFO 32091 Cercophora coprophila B AY999136 AY999112 AY999141
SMH 3794 Cercophora coprophila B AY780058 AY780102 AY780162
CBS 120013T Cercophora grandiuscula B GQ922544 MT731524 MT731530 MT731562
ATCC 200395 Cercophora terricola B AY780067 AY780109 AY780170
CBS 180.66T Cladorrhinum foecundissimuma B MK926856 FR692343 KT291717/MK926956 MK876818
CBS 182.66 Cladorrhinum foecundissimuma B MH858768
BCCM 6980 Cladorrhinum foecundissimuma B KT321080 KT312993 KT291721
CGMCC3.17921 Cladorrhinum globisporum B KY883234
LC5415 Cladorrhinum globisporum B KU746680 KU746726 KU746771
TTI-313 Podospora australis B KX015765 KX015765
LyRS93415 Podospora australis B KF557696
LyRS92471 Podospora australis B KF557695
CBS 322.70T Thielavia hyalocarpa B MK926857 MK926857 MK926957 MK876819
CBS 102198 Thielavia hyalocarpa B MK926858 MK926858 MK926958 MK876820
CBS 433.96T Thielavia intermedia B MK926859 MK926859 MK926959 MK876821
CBS 100257 Thielavia intermedia B MK926860 MK926860 MK926960 MK876822
CBS 389.84 Zopfiella leucotricha B 982801b MT731523 MT731560
CBS 463.61 Zopfiella leucotricha B MH858107 MH869684
CGMCC 3.15230 Apiosordaria hamata C KP878306 KP878304
NBRC 30406 Apiosordaria jamaicensis C 3040601b 3040601b
CBS 672.70T Apiosordaria jamaicensis C MH859895 MT731527 MT731534 MT731556
FMR 6363 Apiosordaria nigeriensis C AJ458184
CBS 713.70T Apiosordaria sacchari C MH859915 KP981425 KP981552 KP981607
CBS 259.71T Apiosordaria spinosa C MH877809
CBS 154.77 Apiosordaria striatispora C MH861043 MT731529 MT731559
CBS 258.71T Apiosordaria tuberculata C MH860107 MH871882
SMH 4021 Cercophora costaricensis C AY780059 AY780103 AY780163
SMH 3200 Cercophora sp. C AY780055 AY780098 AY780159
INTA-AR 70T Cladorrhinum australe C KT321062 KT312976 KT291700
CBS 304.90T Cladorrhinum bulbillosum C MK926861 MK926861 MK926961 MK876823
CBS 126090T Cladorrhinum flexuosum C MH864075 FN662477
CBS 303.90 Cladorrhinum samala C FM955447 FR692338
CBS 302.90 Cladorrhinum samala C KT312992 KT291719
NBRC 107619 Cladorrhinum sp. C 12744402b 12744401b
CBS 482.64T Podospora fimiseda a C MK926862 MT731525 MK926962 MT731531 MT731557
CBS 990.96 Podospora fimiseda a C AY515361 AY346296 MK926963 AY780133 AY780190
CBS 257.71 Zopfiella inermis C MT731526 MT731533 MT731555
CBS 286.86T Zopfiella macrospora C MH861958 MT731528 MT731532 MT731558
CBS 643.75AT Cladorrhinum brunnescens FM955446 FR692346
Outgroups
CBS 148.51 Chaetomium globosum a Out Genomic Genomic Genomic Genomic Genomic
CBS 160.62 Chaetomium globosum a Out KT214565 KT214596 KT214742 KT214666
FMR 13414 Diplogelasinospora princeps a Out KP981431 KP981559 KP981614
SMH 1538 Lasiosphaeria ovina a Out AF064643 AF466046 AY600287
SMH 4106 Sordaria fimicola a Out AY780079 AY780138 AY780194
CBS 230.78 Zopfiella tabulataa Out MK926854 MK926854 MK926954 MK876816
CBS 120402 Cercophora mirabilisa Out KP981429 KP981556 KP981611

Phylogenetic analyses

Each locus was aligned using the online server of MAFFT v. 7.467 (https://mafft.cbrc.jp/alignment/server/; (Katoh et al. 2019) with default settings, followed by manual curation adjusting for the coding frame of the protein-coding markers. We concatenated all alignments and performed a Maximum Likelihood analysis using IQ-TREE v 1.6.8 (Nguyen et al. 2015; Kalyaanamoorthy et al. 2017) with an extended model selection (-m MFP) and 100 standard bootstrap pseudo-replicates. In addition, each individual marker and combinations of markers were analysed as above, but only including sequences that were at least 45% as long as the locus alignment and/or larger than 250 bp. Only strains that consistently showed membership to the Podosporaceae are presented here. The isolates Podospora brasiliensis CBS 892.96, Podospora inflatula CBS 412.78 and P. inflatula CBS 413.82 likely belong to the family, but were excluded due to inconsistent affinities of markers.

Evaluating phylogenetic signal

To evaluate the phylogenetic signal in our datasets, we followed the approach of Shen et al. (2017), which quantifies the amount of support of particular sites or entire genes for two alternative topologies with respect to a particular branch (termed T1 and T2). We set T1 as the Maximum Likelihood topology produced with the concatenated alignment of all markers and T2 as a topology inferred in the same way but constrained to maintain the Clades A and C (see Results) as sisters. To determine what topology is the most supported for each site of each marker, we calculated the site-wise log-likelihood score using RAxML v. 8.2.12 (Stamatakis 2014) with the options -f G -m GTRGAMMA. The output was processed with the scripts 1_sitewise_analyzer.pl and 2_genewise_analyzer.pl (Shen et al. 2017) and additional custom scripts available as a full Snakemake (Köster and Rahmann 2018) pipeline at https://github.com/SLAment/Podosporaceae. As a result, we obtained the gene-wise log-likelihood score of each gene for either T1 or T2 and compared them by calculating their difference in likelihood (ΔGLS) following Shen et al. (2017).

Results

Our complete dataset contains 107 taxa and 5895 sites, of which 2110 are variable and 1654 are parsimony informative (Suppl. material 5: Table S2: Supplementary_Table2_Markers). However, combined datasets have a considerable amount of missing data due to the sparse availability of markers for most species. In agreement with previous studies, Maximum Likelihood analyses of all markers reveal that three well-supported clades are resolved within the family, referred to here as Clade A, Clade B and Clade C (Fig. 1; see also Suppl. material 1: Fig. S1 ITSLSU.min0.45–250, Suppl. material 2: Fig. S2 Btub1_and_2.min0.45–250 and Suppl. material 3: Fig. S3 rpb2.min0.45–250). The exception is Btub1 and Btub2, alone or combined, which tend to place members of the outgroup within the ingroup (Suppl. material 2: Fig. S2 Btub1_and_2.min0.45–250). The taxon Cladorrhinum brunnescens appears to represent a distinct lineage within the family, but this finding is only based on the rDNA markers, as no other markers are available for this taxon. None of the main clades of the combined dataset shows monophyly for any genera included in the analyses and, for some species, like Arnium olerum, representative strains appear to be highly divergent. The focal species of this paper, P. anserina, falls within Clade A (Fig. 2), whereas the type species of Podospora, P. fimiseda, is in Clade C (Fig. 3). While each clade itself is generally well supported for individual markers and combinations of markers, the relationships between the clades are not (Suppl. material 1: Fig. S1 ITSLSU.min0.45–250, Suppl. material 2: Fig. S2 Btub1_and_2.min0.45–250 and Suppl. material 3: Fig. S3 rpb2.min0.45–250). The combined analysis of all markers shows support for the sister relationship of Clades A and B, as reported previously by Wang et al. (2019), but this topology seems to be driven exclusively by the rpb2 marker (Fig. 1). A concatenated analysis of all markers, excluding rpb2, recovers a sister relationship between Clades A and C instead, albeit poorly supported. Except for rpb2, individual markers have generally low ΔGLS values (that is, the difference in likelihood between competing topologies is small), indicating that they have relatively low support for either potential sister relationship (AB or AC). By contrast, rpb2 is strongly biased towards the AB hypothesis (Fig. 4A). Notably, the majority of sites for most markers have higher support for the AC relationship, including rpb2 (Fig. 4B). This suggests that the AC clustering is often favoured by any given site, but only weakly (i.e. the difference in likelihood is very small). Although less frequent, the sites in rpb2 that do support the AB relationship have a large likelihood difference between topologies and likely drive the overall positive ΔGLS value of this gene. Thus, the strong degree of conflict between markers for this internode seems to be driven by a single gene with strong phylogenetic signal (rpb2) and for several other markers without sufficient phylogenetic signal.

Figure 1. 

Schematic phylogenetic relationships of the main clades within the Podosporaceae based on Maximum Likelihood analyses of concatenated markers. The three main clades (A, B and C) are strongly supported (bootstrap support values next to relevant branches), but their particular relationship changes depending on the presence of the rpb2 marker. Branches proportional to the scale bar (nucleotide substitutions per site).

Figure 2. 

Maximum Likelihood phylogeny of the concatenated analysis of ITS, LSU, Btub and rpb2 for the Podosporaceae, with an emphasis on Clade A. Type strains are indicated with a bold T and those of the focal species Podospora anserina and Triangularia bambusae are highlighted with coloured boxes. Bootstrap support values are depicted next to their respective branches, but values corresponding to nearly identical sequences are removed for clarity. Branches are proportional to the scale bar (nucleotide substitutions per site).

Figure 3. 

Maximum Likelihood phylogeny of the concatenated analysis of ITS, LSU, Btub and rpb2 for the Podosporaceae, with an emphasis on the clades B and C. Type strains are indicated with a bold T and that of the focal species Podospora fimiseda is highlighted with a coloured box. Bootstrap support values are depicted next to their respective branches, but values corresponding to nearly identical sequences are removed for clarity. Branches are proportional to the scale bar (nucleotide substitutions per site).

Figure 4. 

Phylogenetic signal in the available molecular markers for the relationship between clade A and either clade B or C of the Podosporaceae A differences in the gene-wise log-likelihood scores (ΔGLS) for each marker, where 0 implies equal support for either of the two alternative sister relationships (A and B or A and C), positive values mean higher support for A and B and negative values higher support for A and C B proportion of sites that support each of the two sister relationships within each marker.

Discussion

With the widespread use of molecular markers to determine the phylogenetic relationships among species, numerous important fungal groups have faced taxonomic challenges including Cryptococcus (Hagen et al. 2015; Kwon-Chung et al. 2017), Zymoseptoria (Quaedvlieg et al. 2011), Fusarium (Geiser et al. 2013), Magnaporthe (Zhang et al. 2016) and Ustilago (McTaggart et al. 2016; Thines 2016), many of which remain unresolved. Fungi are, of course, not the only group whose phylogenetic and taxonomic concepts are in conflict; the model insect genus, Drosophila, is still embroiled in a nomenclatural controversy that has yet to be satisfactorily resolved (O’Grady and Markow 2009; Johnson 2018). In the case presented before us, the issue is, in fact, not so complex as most of these other examples. The taxonomic assignments amongst species and strains of the Sordariales has long been recognised as a difficult problem, with various authors seeking to provide some clarity (Huhndorf et al. 2004; Miller and Huhndorf 2005; Félix 2015; Kruys et al. 2015). It is clear that previous use of morphological characters to designate genera has failed to resolve monophyletic groups, as all genera represented here are not only distributed amongst the three clades within the Podosporaceae, but can also be found in the much more distantly-related clades (Lasiosphaeriacceae I–III sensu Kruys et al. (2015)). It is thus apparent that the way forward is to define the genera based on molecular phylogenies.

While previous phylogenetic analyses on the Sordariales in general have been informative, the lack of resolution remains a pervasive issue (e.g. Kruys et al. 2015). Our results suggest that the molecular markers, typically used for the study of this group, have a relatively low phylogenetic signal for a number of key internodes. Within Podosporaceae, in particular, the relationship between the clades containing P. anserina and P. fimiseda (clades A and C) is crucial to decide on an optimal naming scheme that minimises taxonomic and practical conflict. Additionally, throughout the phylogeny, there are a number of strains that have been assigned to different species and genera, but likely belong to the same species (e.g. Thielavia hyalocarpa and Zopfiella leucotricha strain CBS389.84 are identical for ITS and LSU). Additionally, there appears to be undiscovered sexual states of the anamorphic Cladorrhinum species, like C. foecundissimum with the A. olerum strain CBS120012. Taxonomic re-assignments of these groups should be undertaken; however, without a strong phylogenetic backbone, based on multiple genes and an expanded taxonomic sampling, it seems premature to propose nomenclatural changes.

In recent years, a number of authors have established the use of time-calibrated phylogenies to define ranks from genus up to class for various groups of fungi, although this approach has not been without controversy (Lücking 2019). For the Sordariomycetes, intervals of 150–250 MYA for orders and 50–150 MYA for families have been recommended (Hyde et al. 2017). Both the Sordariales and the Podosporaceae agree well with these values with estimated divergence times of 109.69 MYA and < 76.58 MYA, respectively (Lutzoni et al. 2018), although a comprehensive investigation of divergence amongst the Lasiosphaeriaceae has yet to be conducted. The use of time-calibrated trees to define genera is less common, but a divergence time of ~30 MYA has been suggested previously (Divakar et al. 2017). In this regard, it would be appropriate to define the three clades presented herein as genera as Wang et al. (2019) have done, based on divergence times between Lasiosphaeria ovina and Anopodium ampullaceum (Hyde et al. 2017), which show similar phylogenetic distances between each other as the three clades of Podosporaceae (Félix 2015). However, time-calibrated phylogenies need not and often should not, set the standard for taxonomic delimitation. One telling example comes from the field of Fusarium research. When the ‘one name one fungus’ edict came into effect, it threatened to divide a cosmopolitan group of plant pathogenic fungi that are united in their vegetative morphology and pathophysiology into several genera. To combat this issue, the field pushed for the usage of Fusarium for the entire group, despite considerable phylogenetic distance (Geiser et al. 2013). As a result, Fusarium encompasses species which diverged more than ~70 MYA (Lutzoni et al. 2018), yet this move ensured the nomenclatural stability of the organisms in question.

When proposing new combinations, one should always ensure to make decisions that will cause the least amount of confusion in literature. In this case, it is clear that, for this goal, the name P. anserina should be preserved. Google Scholar returns ~11500 hits to the search query Podospora anserina, yet only ~2110 hits for Triangularia, the majority of which are due to the use of the word “triangularia” in Latin and have no relation to the genus. There are currently 62967 sequences in Genbank with Podospora anserina in the title, while only 76 contain Triangularia in the title and lastly, the English Wikipedia page for Podospora anserina has had 13897 page views from July 2015 to May 2020, while the English Wikipedia Triangularia page has had only 705 views over the same period. The best possible way forward to prevent the re-naming of P. anserina or the subsequent instability it will cause in literature is to transfer the type of Podospora from P. fimiseda to P. anserina, despite P. fimiseda having been conserved over Schizothecium fimicola Corda (Proposal 119). Unfortunately, this process can take many years of debate and the re-assignment of P. anserina to Triangularia already threatens a peaceful transition. At the very least, if P. anserina needs to be assigned to another genus, it should be the type species of that genus in order to prevent further potential nomenclatural changes. Thus, we propose, for the interim, to synonymise Triangularia with Podospora until a more satisfactory resolution can be made. Once more data are available, it will hopefully be possible to resolve the relationships amongst the three clades. If, in the end, Clade A and B are found to be sisters, then it would require that Cladorrhinum sensu Wang et al. (2019) (Clade B here) be synonymised with Podospora as well. Alternatively, if Clade A and C are sisters, then Podospora could be restricted to these two clades and fewer taxonomic changes would be required. As we ultimately aim to move the type species of Podospora to P. anserina, we will refrain from making any new combinations at the moment.

In the previous example with Fusarium, a divergent group of fungi were classified under one name precisely because the researchers in that field desired unity. In the case of Podospora, the only factor necessitating that disparate species fall under one genus is the need to operate within the confines of the ICN. The ultimate goal of the code is to provide taxonomic stability and conformity to the organisms it covers. The nature of studying microscopic fungi has resulted in numerous names with dubious origins and, while obvious fixes are sometimes evident, they are not always possible to enact according to the ICN. It is understandable why the current code is as rigid as it is, but the current editions have seen it become more flexible, which has been advantageous to many fields seeking to solidify tumultuous taxonomy. In the future, we hope that additional data and a permissive code will allow us to enshrine the name Podospora anserina indefinitely, settling over a century of nomenclatural friction between taxonomists and other researchers.

Taxonomy

Podospora Ces., Hedwigia 1(15): 103 (1856)

MycoBank No: 4284

Type species

Podospora fimiseda (Ces. & De Not.) Niessl, Hedwigia 22: 156 (1883).

Syn: Apiosordaria Arx & W. Gams, Nova Hedwigia 13: 201 (1967).

Syn: Triangularia Boedijn, Annls mycol. 32(3/4): 302 (1934).

Syn: Lacunospora Cailleux, Cahiers de La Maboké 6(2): 93 (1969) [1968].

Syn: Tripterospora Cain, Can. J. Bot. 34: 700 (1956).

Syn: Philocopra Speg., Anal. Soc. cient. argent. 9(4): (1880).

Syn: Malinvernia Rabenh., Hedwigia 1: 116 (1857).

Syn: Pleurage Fr., Summa veg. Scand., Sectio Post. (Stockholm): 418 (1849).

Acknowledgements

We would like to thank Lymari Ruiz for their assistance in generating the sequence data, to Iker Irisarri for his guidance with the phylogenetic analysis, and Martin Ryberg and Mats Thulin for their advice on taxonomic issues. We would like to thank the Swedish Research Council and Formas for research funds. We would also like to acknowledge past and present researchers who have devoted much of their time to the study of Podospora anserina to elevate it to the status of model organism.

References

  • Couturier M, Tangthirasunun N, Ning X, Brun S, Gautier V, Bennati-Granier C, Silar P, Berrin J-G (2016) Plant biomass degrading ability of the coprophilic ascomycete fungus Podospora anserina. Biotechnology Advances 34: 976–983. https://doi.org/10.1016/j.biotechadv.2016.05.010
  • Divakar PK, Crespo A, Kraichak E, Leavitt SD, Singh G, Schmitt I, Lumbsch HT (2017) Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi. Fungal Diversity 84: 101–117. https://doi.org/10.1007/s13225-017-0379-z
  • Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury J-M, Ségurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Déquard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarré B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P (2008) The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology 9: R77. https://doi.org/10.1186/gb-2008-9-5-r77
  • Félix YM (2015) Soil ascomycetes from different geographical regions. Universitat Rovira i Virgili, Spain.
  • Fitzpatrick DA, Logue ME, Stajich JE, Butler G (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology 6: 1–99. https://doi.org/10.1186/1471-2148-6-99
  • Geiser DM, Aoki T, Bacon CW, Baker SE, Bhattacharyya MK, Brandt ME, Brown DW, Burgess LW, Chulze S, Coleman JJ, Correll JC, Covert SF, Crous PW, Cuomo CA, De Hoog GS, Di Pietro A, Elmer WH, Epstein L, Frandsen RJN, Freeman S, Gagkaeva T, Glenn AE, Gordon TR, Gregory NF, Hammond-Kosack KE, Hanson LE, del Mar Jímenez-Gasco M, Kang S, Corby Kistler H, Kuldau GA, Leslie JF, Logrieco A, Lu G, Lysøe E, Ma L-J, McCormick SP, Migheli Q, Moretti A, Munaut F, O’Donnell K, Pfenning L, Ploetz RC, Proctor RH, Rehner SA, Vincent AR, Rooney AP, Salleh BB, Scandiani MM, Scauflaire J, Short DPG, Steenkamp E, Suga H, Summerell BA, Sutton DA, Thrane U, Trail F, Van Diepeningen A, VanEtten HD, Viljoen A, Waalwijk C, Ward TJ, Wingfield MJ, Xu J-R, Yang X-B, Yli-Mattila T, Zhang N (2013) One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 103: 400–408. https://doi.org/10.1094/PHYTO-07-12-0150-LE
  • Grognet P, Timpano H, Carlier F, Aït-Benkhali J, Berteaux-Lecellier V, Debuchy R, Bidard F, Malagnac F (2019) A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina. PLoS genetics 15: e1008086. https://doi.org/10.1371/journal.pgen.1008086
  • Hagen F, Khayhan K, Theelen B, Kolecka A, Polacheck I, Sionov E, Falk R, Parnmen S, Lumbsch HT, Boekhout T (2015) Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genetics and Biology: FG & B 78: 16–48. https://doi.org/10.1016/j.fgb.2015.02.009
  • Hyde KD, Maharachchikumbura SSN, Hongsanan S, Samarakoon MC, Lücking R, Pem D, Harishchandra D, Jeewon R, Zhao R-L, Xu J-C, Liu J-K, Al-Sadi AM, Bahkali AH, Elgorban AM (2017) The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday. Fungal Diversity 84: 1–23. https://doi.org/10.1007/s13225-017-0383-3
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587–589. https://doi.org/10.1038/nmeth.4285
  • Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
  • Kruys Å, Huhndorf SM, Miller AN (2015) Coprophilous contributions to the phylogeny of Lasiosphaeriaceae and allied taxa within Sordariales (Ascomycota, Fungi). Fungal Diversity 70: 101–113. https://doi.org/10.1007/s13225-014-0296-3
  • Kwon-Chung KJ, Bennett JE, Wickes BL, Meyer W, Cuomo CA, Wollenburg KR, Bicanic TA, Castañeda E, Chang YC, Chen J, Cogliati M, Dromer F, Ellis D, Filler SG, Fisher MC, Harrison TS, Holland SM, Kohno S, Kronstad JW, Lazera M, Levitz SM, Lionakis MS, May RC, Ngamskulrongroj P, Pappas PG, Perfect JR, Rickerts V, Sorrell TC, Walsh TJ, Williamson PR, Xu J, Zelazny AM, Casadevall A (2017) The case for adopting the “species complex” nomenclature for the etiologic agents of cryptococcosis. mSphere 2. https://doi.org/10.1128/mSphere.00357-16
  • Lücking R (2019) Stop the abuse of time! Strict temporal banding is not the future of rank-based classifications in Fungi (Including lichens) and other organisms. Critical Reviews in Plant Sciences 38: 199–253. https://doi.org/10.1080/07352689.2019.1650517
  • Lundqvist N (1972) Nordic Sordariaceae s. lat. Symbolae Botanicae Upsalienses 20: 1–374.
  • Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S (2018) Contemporaneous radiations of fungi and plants linked to symbiosis. Nature Communications 9: 1–5451. https://doi.org/10.1038/s41467-018-07849-9
  • McTaggart AR, Shivas RG, Boekhout T, Oberwinkler F, Vánky K, Pennycook SR, Begerow D (2016) Mycosarcoma (Ustilaginaceae), a resurrected generic name for corn smut (Ustilago maydis) and its close relatives with hypertrophied, tubular sori. IMA Fungus 7: 309–315. https://doi.org/10.5598/imafungus.2016.07.02.10
  • Miller AN, Huhndorf SM (2005) Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi). Molecular Phylogenetics and Evolution 35: 60–75. https://doi.org/10.1016/j.ympev.2005.01.007
  • Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268–274. https://doi.org/10.1093/molbev/msu300
  • Quaedvlieg W, Kema GHJ, Groenewald JZ, Verkley GJM, Seifbarghi S, Razavi M, Mirzadi Gohari A, Mehrabi R, Crous PW (2011) Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts. Persoonia – Molecular Phylogeny and Evolution of Fungi 26: 57–69. https://doi.org/10.3767/003158511X571841
  • Saupe SJ, Clavé C, Bégueret J (2000) Vegetative incompatibility in filamentous fungi: Podospora and Neurospora provide some clues. Current opinion in microbiology 3: 608–612. https://doi.org/10.1016/S1369-5274(00)00148-X
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109: 6241–6246. https://doi.org/10.1073/pnas.1117018109
  • Shen X-X, Hittinger CT, Rokas A (2017) Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution 1. https://doi.org/10.1038/s41559-017-0126
  • Silar P, Dauget J-M, Gautier V, Grognet P, Chablat M, Hermann-Le Denmat S, Couloux A, Wincker P, Debuchy R (2019) A gene graveyard in the genome of the fungus Podospora comata. Molecular Genetics and Genomics 294: 177–190. https://doi.org/10.1007/s00438-018-1497-3
  • Thines M (2016) (2467) Proposal to conserve the name Ustilago (Basidiomycota) with a conserved type. Taxon 65: 1170–1171. https://doi.org/10.12705/655.20
  • Turland NJ, Greuter W, Turland NJ, Wiersema JH, Kusber W-H, Barrie FR, Hawksworth DL, Herendeen PS, Knapp S, Marhold K, Li D-Z, McNeill J, May TW, Munro AM, Prado J, Price MJ, Smith G (2018) International code of nomenclature for algae, fungi, and plants (Shenzhen code): adopted by the nineteenth international botanical congress, Shenzhen, China, July, 2017, 254 pp. https://doi.org/10.12705/Code.2018
  • van der Gaag M, Debets AJ, Oosterhof J, Slakhorst M, Thijssen JA, Hoekstra RF (2000) Spore-killing meiotic drive factors in a natural population of the fungus Podospora anserina. Genetics 156: 593–605.
  • van der Gaag M, Debets AJ, Osiewacz HD, Hoekstra RF (1998) The dynamics of pAL2-1 homologous linear plasmids in Podospora anserina. Molecular & General Genetics 258: 521–529. https://doi.org/10.1007/s004380050763
  • Vogan AA, Lorena Ament-Velásquez S, Bastiaans E, Wallerman O, Saupe SJ, Suh A, Johannesson H (2020) The Enterprise: A massive transposon carrying Spok meiotic drive genes. BioRxiv. https://doi.org/10.1101/2020.03.25.007153
  • Vogan AA, Lorena Ament-Velásquez S, Granger-Farbos A, Svedberg J, Bastiaans E, Debets AJM, Coustou V, Yvanne H, Clavé C, Saupe SJ, Johannesson H (2019) Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 8. https://doi.org/10.7554/eLife.46454
  • Wang XW, Bai FY, Bensch K, Meijer M, Sun BD, Han YF, Crous PW, Samson RA, Yang FY, Houbraken J (2019) Phylogenetic re-evaluation of Thielavia with the introduction of a new family Podosporaceae. Studies in Mycology 93: 155–252. https://doi.org/10.1016/j.simyco.2019.08.002
  • Zhang N, Luo J, Rossman AY, Aoki T, Chuma I, Crous PW, Dean R, de Vries RP, Donofrio N, Hyde KD, Lebrun M-H, Talbot NJ, Tharreau D, Tosa Y, Valent B, Wang Z, Xu J-R (2016) Generic names in Magnaporthales. IMA fungus 7: 155–159. https://doi.org/10.5598/imafungus.2016.07.01.09

Supplementary materials

Supplementary material 1 

Figure S1

S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J.M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

Data type: statistical data

Explanation note: Maximum Likelihood phylogeny of the concatenated analysis of ITS and LSU. Type strains of the focal species are highlighted with coloured boxes. Bootstrap support values are depicted next to their respective branches, but values corresponding to nearly identical sequences are removed for clarity. Branches are proportional to the scale bar (nucleotide substitutions per site). Clades are marked with lateral bars following the topology in Figure 1.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (19.38 kb)
Supplementary material 2 

Figure S2

S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J.M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

Data type: statistical data

Explanation note: Maximum Likelihood phylogeny of Btub1 and Btub2 separately. The outgroup taxa are not resolved as monophyletic and, hence, the rooting was arbitrarily chosen. Type strains of the focal species are highlighted with coloured boxes. Bootstrap support values are depicted next to their respective branches, but values corresponding to nearly identical sequences are removed for clarity. Branches are proportional to the scale bar (nucleotide substitutions per site). Clades are marked with lateral bars, following the topology in Figure 1.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (17.03 kb)
Supplementary material 3 

Figure S3

S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J.M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

Data type: statistical data

Explanation note: Maximum Likelihood phylogeny of rpb2. Type strains of the focal species are highlighted with coloured boxes. Bootstrap support values are depicted next to their respective branches, but values corresponding to nearly identical sequences are removed for clarity. Branches are proportional to the scale bar (nucleotide substitutions per site). Clades are marked with lateral bars, following the topology in Figure 1.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (15.31 kb)
Supplementary material 4 

Table S1

S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J.M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

Data type: molecular data

Explanation note: List of primers used to generate sequence data.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (23.50 kb)
Supplementary material 5 

Table S2

S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J.M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

Data type: statistical data

Explanation note: Analysed data matrices.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (20.50 kb)