Among the several Sordariomycetes fungi that have been utilized as models, N. crassa is perhaps the most widely examined, and was the first multicellular fungus to have its genome sequenced and annotated (Borkovich et al., 2004; Dunlap et al., 2007). It is a non-pathogenic saprotroph that grows vegetatively and can be cultured in most defined and natural media, and, as such, remains a widely used model that facilitates research across a worldwide community, which has addressed a broad range of questions in general and fungal biology (Perkins, 1992). The species has a distinguished history, including its role in the formulation of the “one gene—one enzyme” hypothesis proposed by Beadle and Tatum (1941).

Closely related to N. crassa, N. tetrasperma is pseudohomothallic and employs a mating strategy that combines selfing with occasional outbreeding (Merino et al., 1996; Sun et al., 2017). N. tetrasperma provides a model for study of both the genomic and the evolutionary consequences of asexuality and inbreeding (Sun et al., 2012; Samils et al., 2013; Idnurm et al., 2015). These consequences cannot be studied in obligate outbreeders alone, such as N. crassa and other popular genetic models. A pangenomic analysis of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma has provided experimental evidence for the role of introgression as a mechanism for the maintenance of mating-type-determining chromosomal regions (Corcoran et al., 2016).

Interestingly, Neurospora species are also known as postfire fungi, as they are often spotted in the forest after a fire, a unique environment shared with certain other pyrophilous fungi (Hansen and Pfister, 2006; Wicklow, 2018), such as Geopyxis carbonaria (Pyronemataceae, Pezizales) and some species of Pyronema and Peziza (Pezizales). Another easily maintained and genetically manipulated species, Podospora anserina, has long been used as a model to study aging, meiosis, sexual reproduction, and heterokaryon formation in fungi (Philipp et al., 2013; Silar et al., 2019; Hartmann et al., 2021a; Lelandais et al., 2022). P. anserina and N. crassa genomes share over 60%–70% similarity in orthologous proteins, making them a powerful pair of models that can be used as references for comparative genomics (Espagne et al., 2008; Paoletti and Saupe, 2008).

Yet another intensively studied developmental genetic model in the Sordariomycetes is S. macrospora, with over 100 available developmental mutants (Nowrousian et al., 2010; Nowrousian et al., 2012; Blank-Landeshammer et al., 2019; Teichert et al., 2020). Similar to species of Neurospora and Podospora, S. macrospora grows quickly under laboratory conditions. The fact that S. macrospora is homothallic can be advantageous for sexual and developmental synchronization and for maintenance of a homogeneous genetic background.

A small number of Sordariomycetes fungi, including Fusarium and Magnaporthe species, are models for fungal pathogenesis; over the past decades, Fusarium research has advanced our understanding of these fungi. Fusarium is a large genus, including some anamorphic fungi, for which sexual development and reproduction has never been observed (O’Donnell et al., 2015). This genus harbors important plant pathogens, producers of a wide range of fungal chemicals, and causal agents of opportunistic mycoses in humans (Suga and Hyakumachi, 2004). F. graminearum sensu lato is a species complex whose members cause devastating diseases in small grains and mycotoxin contamination worldwide (Wang et al., 2010; Wang et al., 2011; Garmendia et al., 2018; Chai et al., 2022; Del Ponte et al., 2022). F. graminearum sensu stricto refers to the major disease-causing species in the USA (and a few other places); as this was the subject of one of the first genomics projects (Cuomo et al., 2007), it has since been frequently used in many comparative studies (Khan et al., 2020; Rampersad, 2020; Teli et al., 2020). This fungus has been intensively studied as a cosmopolitan model for fungal pathogenesis of crop plants. The largest source of inoculum for disease outbreaks originates from the primary inoculum, airborne sexual spores (forcibly discharged from fruiting bodies), with aboveground asexual spores (mainly splash-dispersed) providing a local secondary inoculum (Ingold and Dring, 1957). For this reason, the species F. graminearum has become a model for the study of perithecium development on host plants (Kim et al., 2022) and the mechanism of forcible ascospore discharge (Trail et al., 2005; Trail, 2007; Cavinder et al., 2012; Trail and Seminara, 2014; David et al., 2016). Recently, F. graminearum has become the first plant-pathogenic fungus documented to produce biofilms in association with plant colonization (Shay et al., 2022). Although fungicide applications are the main source of control over the disease, there are no strongly resistant varieties of wheat or barley available. In addition to being infamous crop pathogens, Fusarium spp. are also considered to be severe threats to human health and are listed in the WHO fungal priority pathogens list to guide research, development, and public health action (World Health Organization, 2022; Rodrigues and Nosanchuk, 2023). As in the case of Neurospora spp., comparative genomic analysis of Fusarium spp. has also been instrumental to the field’s understanding of the evolution of sexual development (Trail et al., 2017). One example is the identification and analysis of horizontally transferred lineage-specific genomic regions related to pathogenicity (Ma et al., 2010).

Magnaporthe species cause devastating crop diseases. M. grisea, the causal agent of rice, was sequenced in 2005 (Dean et al., 2005). Rice blast causes significant economic loss: worldwide, enough rice to feed tens of millions of people is destroyed by rice blast every year (Kumar et al., 2020). Closely related to M. grisea, M. oryzae attacks wheat, causing wheat blast, an emergent fungal disease that probably evolved through a series of “host jumps” and that possesses core chromosomes and mini-chromosomes with distinct evolutionary histories (Hossain, 2022). A genomic surveillance study of over 500 strains from diverse geographic regions and host types has revealed the adaptation and development of fungicide resistance in a pandemic clonal lineage of M. oryzae (Latorre et al., 2023; Rhodes, 2023). Infections occur when fungal spores land on and invade wheat leaves using an appressorium—a specialized infection cell formed during spore germination. The process of the development of appressoria has recently been investigated intensively using genome-wide analysis (Lv et al., 2022; Wang et al., 2022a; Fan et al., 2023; Miguel-Rojas et al., 2023; Qian et al., 2023; Rogers and Egan, 2023). Diverse ecologies have been reported for species of the Magnaporthales, ranging from saprotrophs to cereal pathogens to likely root endophytes (Luo et al., 2015). The Sordariomycetes also include diverse entomopathogenic fungi, including the “zombie” fungus genus Cordyceps and the species of Beauveria (Cordycipitaceae, Hypocreales) and Metarhizium (Cordycipitaceae, Hypocreales), commonly used as biopesticides of pathogenic insects and arthropods. Omics-based investigation of these fungi is expanding rapidly (Zheng et al., 2011; Xiao et al., 2012; Pattemore et al., 2014; Valero-Jiménez et al., 2016; Wang et al., 2016a; Chen et al., 2019; Kato et al., 2022; Thananusak et al., 2022; Liu and Dong, 2023). Interestingly, some fungi, such as Metarhizium species, are capable of attacking hosts in both the plant and the animal kingdoms.

In addition to plant, arthropod, and human hosts, the Sordariomycetes also include a unique pathogenic group, mycoparasites, capable of parasitizing other fungi, including both pathogenic and economically beneficial species. These include species such as Clonostachys rosea (Hypocreales; Bionectriaceae), Calcarisporium cordycipiticola (Hypocreales; Calcarisporiaceae), Lecanicillium fungicola (Hypocreales; Cordycipitaceae), Syspastospora parasitica (Hypocreales; Hypocreaceae), and Escovopsis weberi (Hypocreales; Hypocreaceae) (Posada et al., 2004; Berendsen et al., 2010; de Man et al., 2016; Sun et al., 2020; Liu et al., 2021). Over the years, significant attention has been given to the study of mycoparasites belonging to the genus Trichoderma, which contains many species of significant value to agriculture and industry, and the genomics of which have been comprehensively examined (Schalamun and Schmoll, 2022). Trichoderma reesei is a unique species among other industrial fungi (Seidl et al., 2009; Druzhinina et al., 2011). T. reesei (teleomorphic; Hypocrea jecorina) is a known industrial cellulolytic enzyme producer, making it a model system for the study of the regulatory mechanisms of plant cell wall-degrading enzymes; this work contributes to the biofuel and agricultural waste industries. T. harzianum, T. asperellum, and T. asperelloides are among the most thoroughly analyzed Trichoderma spp. and have been incorporated in biocontrol strategies (Druzhinina et al., 2011). These biocontrol species and other Trichoderma strains have been demonstrated to successfully control plant diseases by stimulating plant growth and development, increasing plant resistance to biotic and abiotic stresses, and directly parasitizing phytopathogenic fungi (Zeilinger and Omann, 2007; Atanasova, 2014; Guzmán-Guzmán et al., 2019; Poveda, 2021; Di Lelio et al., 2023; Woo et al., 2023). Moreover, T. reesei and T. asperellum are considered to be models for the industrial production of various secondary metabolites (Mukherjee et al., 2013; Schalamun and Schmoll, 2022) and biofungicides due to their mycoparasitic properties, which benefit plants challenged by other fungal pathogens (Kubicek et al., 2011).

The first full Trichoderma genome analyzed was that of T. reesei (Martinez et al., 2008). T. asperellum and T. asperelloides (along with others) were analyzed later (Berka, 2017; Druzhinina et al., 2018; Gortikov et al., 2022a), well after the genomes of Neurospora and Fusarium species (Druzhinina et al., 2018). The recently sequenced genome of T. asperelloides contributed to the determination of its correct taxonomic identity, in contrast to its previous identification as the closely related T. asperellum, a model for biological control (Podder and Ghosh, 2019; Gortikov et al., 2022a). Currently, there are more than 90 Trichoderma genomes that have been sequenced and released, making it among the most sequenced genera in the class; this is an achievement that can be attributed to a combination of industrial and academic efforts. Comparative genomic insight into Trichoderma spp. is fairly recent. However, insights into the core genome of this genus, potential heterothallic reproduction, and the abundance of species-specific orphan genes (Kubicek et al., 2019) have provided a strong foundation for further class-based comparative genomics with other Sordariomycetes. One species of Sordariomycetes, Calcarisporium cordycipiticola (Calcarisporiaceae, Hypocreales), is a mycoparasite of Cordyceps militaris; mycoparasitism causes devastating diseases of fruiting cultivation. Phylogenomic analysis has highlighted the fact that C. cordycipiticola was evolutionarily close to its host C. militaris, and that they diverged after a split with the Trichoderma genus. Comparative genomic and transcriptome analyses have provided insights into the origin of the pathogen and the mycoparasitic interactions of two species from sister families (Liu et al., 2021; Liu and Dong, 2023).

Dramatic divergences in the development and biology of Sordariomycetes can be observed even among closely related species; thus, the class offers excellent systems for assessment of the molecular genetic basis of the evolution of these species. Among these promising systems, Chaetomium spp. fungi exhibit a frequently homothallic lifestyle, a general lack of asexual reproduction of conidia, enriched secondary metabolism synthesis, and an ability to thrive in highly humid environments (Wang et al., 2016b; Zámocký et al., 2016; Wang et al., 2019a). All of these traits are highly divergent in the genus, rendering these species especially informative regarding rapid evolution in a comparative evolution context. The Chaetomium spp. are cosmopolitan saprotrophs and endophytes that are capable of dominating diverse ecological niches, including some extreme environments, evoking interest in their genomic adaptation for survival and dispersal. Species of Chaetomium are common contaminants in indoor environments and are considered to be health hazards (Andersen et al., 2011; Miller and McMullin, 2014), causing symptoms of rhinitis and asthma when they infect humans (Mackenzie, 1979; Vesper et al., 2007; Hassett et al., 2009; Green et al., 2014). C. globosum is a model for the industrial production of secondary metabolites, and is also generally considered to be a species complex (Asgari and Zare, 2011; Wang et al., 2016b). Chaetomium species probably shared thermophilic ancestors, consistent with the thermophilic basal nature of its most diverged lineage (Zámocký et al., 2016). The genome sequence of C. globosum was made publicly available in 2015 (Cuomo et al., 2015). Since then, the taxonomy and phylogenetics of the genus have been undergoing reassessment and revision (Wang et al., 2022c).

These models represent some of the diverse genera within the Sordariomycetes that have been studied intensively. The availability of many genome sequences that are closely related to established and emerging model species represents a substantial contribution to analyses of the ecological traits of these organisms and their close relatives, which can in turn provide substantial insight. Currently, there are 570 Sordariomycetes genomes (covering 136 genera or high ranks, with more than 330 identified species and 75 unidentified species) in the JGI fungal genome database (mycocosm.jgi.doe.gov/), in addition to the comparative tools available via that portal (Figure 1A). Among these genomes, 189 cover more than 60 species in four genera, including 81 Fusarium and 94 Trichoderma species. Many additional Sordariomycetes genomes are available via the NCBI (National Center for Biotechnology Information), with 3,574 genomes (nearly one-third of the total of 11,083) being published and drafted ascomycetes genomes; these include 1,359 Fusarium, 117 Neurospora, 110 Trichoderma, and 14 Chaetomium genomes. Many of these genomes are for species that are culturable, produce simple morphologies, and are often either pathogenic or economically important. The ecological and industrial relevance of pathogenic members of Sordariomycetes and those producing valuable fungal products has been a major driver of the extensive sequencing of many non-model genomes in this fungal class. Some of these non-model species are emerging as “new” models and, unlike the classic models that have undergone intensive investigation in biology and genetics, established during the pre-genomics era, these species are often studied under a reverse approach, with investigation originating in genomics and then extending to genetics and the analysis of biological traits. For example, the genomes of a large number of species of Xylariale have recently been sequenced, and comparative genomics has revealed genetic changes that are probably associated with bioactivities, diverse lifestyles, environmental adaptations, and selective pressure in these “mystical”-looking fungi (Robinson et al., 2020; Wibberg et al., 2020; Franco et al., 2022; Fricke et al., 2023). At the same time, the annotation of classic model genomes, such as those of Neurospora, Podospora, and Sordaria genomes, has undergone continuous improvement, in part on the basis of information obtained from newly sequenced genomes of the same or closely related species (Teichert et al., 2014; Gladieux et al., 2015; Blank-Landeshammer et al., 2019; Teichert et al., 2020; Lelandais et al., 2022; Rodriguez et al., 2022; Vittorelli et al., 2023). These accumulating data continue to contribute to a new era of evolutionary genomics and transcriptomics at further taxonomic levels within the Sordariomycetes class.

Divergence in gene expression has long been considered to play a critical role in developmental adaptations during organismal evolution (King and Wilson, 1975; Carroll, 2005; Hodgins-Davis et al., 2015; Diaz et al., 2023). The incorporation of divergence in sexual morphology within comparatively closely related taxa could improve the precision and accuracy of reconstructions of ancestral gene expression, yielding expansions to the number of associations between shared morphologies and shared transcriptional profiles. Comparative genomics and evolutionary transcriptomics focusing on Sordariomycetes models has revealed the genes and regulatory networks that are critical for sexual development in these fungi, including non-coding sequences and genes that were previously uncharacterized (Trail et al., 2017; Kim et al., 2018; Kim et al., 2019; Lütkenhaus et al., 2019). In addition, novel genes that affect perithecial development have been identified in M. oryzae and N. crassa, which have diverged functionally and transcriptionally from their orthologous counterparts in F. graminearum (Kim et al., 2022). These novel genes are predicted to be “young” (i.e., present only in a recently diverged clade of species) and tend to be involved in lineage- or species-specific functions. Phenotypic study guided by comparative genomics among three distantly related filamentous fungi has identified two genes (predicted to be chromatin modifiers) that play roles in the sexual development of S. macrospora (Lütkenhaus et al., 2019).

Comparative genomics approaches using these model species have also been pursued in order to understand the evolution of diverse ecologies among the Sordariomycetes, especially those that are related to pathogenesis (Figure 2). Among the pathogenic Sordariomycetes, species of Fusarium have been intensively studied for their diverse genome structures (Brown and Proctor, 2013; Ma et al., 2013; Zhang, 2019; Mir et al., 2023). Research on entomopathogenic Sordariomycetes, represented by Cordyceps, Beauveria, and Metarhizium species, has been greatly enhanced by the availability of genomes of these species (Gao et al., 2011; Pattemore et al., 2014; Valero-Jiménez et al., 2016; Kato et al., 2022; Liu and Dong, 2023; Sant Anna Iwanicki et al., 2023). Neurospora species have been examined as metabolic models of the biodegradation of cellulose and other plant organics (Feldman et al., 2019; Liu et al., 2020; Wu et al., 2020; Huberman et al., 2021), as well as providing some of the most tractable models for the circadian clock and fungal responses to environmental factors, such as light and temperature (Wang et al., 2016c; Dekhang et al., 2017; Wang et al., 2018b; Kelliher et al., 2020; Kelliher et al., 2023). Based on transcriptomics data from N. crassa grown on five different crop residues, researchers have discovered roles for a sporulation regulator rca-1 in lignocellulose production (Wang et al., 2015). Additional roles in allorecognition have also been identified for cwr-1, a putative chitin polysaccharide monooxygenase, in N. crassa (Detomasi et al., 2022). Three studies have investigated the associations between secondary metabolite clusters (SMCs) and reproduction in two fungal models, N. crassa and C. globosum, and reported on the activities of 20 and 24 SMCs in these models, respectively—a manageable set for separate investigation of the roles of SMCs across the life cycle of these two models (Wang et al., 2019a; Wang et al., 2019b; Wang et al., 2022d). Bayesian regulatory networks have been reconstructed using transcriptomic data for N. crassa and C. globosum. These networks exhibit divergences in associations among genes associated with conidiation and heterokaryon incompatibility between N. crassa and C. globosum, supporting the theory that there is an evolutionary history of loss of conidiation in the latter, putatively due to unfavorable combinations of heterokaryon incompatibility in homothallic species. A recent study focused specifically on conidial germination in two model pathogens, F. graminearum and M. oryzae, on artificial medium and on hosts, as conidial germination represents the key stage in the initiation of fungal attack (Miguel-Rojas et al., 2023). The authors’ analyses revealed new and important aspects of early fungal ingress in F. graminearum that can form the basis for improvement of antifungal strategies, including a comparative gene expression finding that toxisomes are not fully functional until after penetration of the host cells. Based on a study using near-synchronous germinating cultures of T. asperelloides (a strain used in biocontrol that was formerly identified as T. asperellum), it has been reported that the transcript abundance of half of the annotated genome is reduced during early conidial germination (Grotikov et al., 2022b). In this study, it was also discovered that the expression of the chitin synthase and glucan elongase families is significantly increased during germination in the presence of a basidiomycete host, Rhizoctonia solani (Ceratobasidiaceae, Cantharellales), indicating that host recognition can occur during the early stages of mycoparasite development (Grotikov et al., 2022b).

Advances in fungal genomics have produced new insights regarding genome evolution in the kingdom. Mycovirus research has greatly benefited from the availability of a large number of fungal genomes and the development of comparative genomics (Kotta-Loizou, 2019; Myers et al., 2020). Mycoviruses have been the focus of biocontrol against fungal pathogens (Yu and Kim, 2020; Schalamun and Schmoll, 2022). More than 10 different families of viruses have been isolated from fungal hosts, including double-stranded RNA (dsRNA), positive-sense and negative-sense single-stranded RNA, and circular single-stranded DNA (ssDNA) viruses (Applen Clancey et al., 2020). The presence of viruses in Fusarium and Trichoderma spp. has been particularly well documented (Yun et al., 2016; Li et al., 2019a; You et al., 2019; Yu and Kim, 2020; Wang et al., 2022b). A recent study investigated the presence of viruses in multiple Neurospora species and identified various RNA viruses from N. crassa and other Neurospora spp. using transcriptomics data. The study further established N. crassa as a virus host model for use in the study of virus–host interactions and virology in fungi (Honda et al., 2020). The authors also demonstrated that N. crassa relies on transcriptional and posttranscriptional regulation to restrict virus replication for at least some of its genes.

Posttranscriptional regulation is another intriguing genome-wide editing mechanism, but how has such a widely distributed mechanism evolved and been maintained across the diverse fungal genome? One example of posttranscriptional regulation is A-to-I editing, which has recently been discovered to be associated with sexual development in filamentous fungi (Bian et al., 2019). Some of these A-to-I-editing filamentous fungi are Sordariomycetes, including N. crassa (Liu et al., 2017), S. macrospora (Teichert et al., 2017), and F. graminearum (Liu et al., 2016). In M. oryzae, N⁶-Methyladenosine (m⁶A) RNA methylation, the most common modification of RNA at the post-transcriptional level in eukaryotes, has been found to be important for various aspects of fungal biology, such as vegetative growth, conidiation, and pathogenicity (Shi et al., 2019). Although disruption of m⁶A factors does not affect sexual development in M. oryzae and F. graminearum, overexpression of the m⁶A writer (the ortholog of the gene coding for IME4 in yeasts) causes delayed sexual development in F. graminearum, suggesting that m⁶A modification may alter developmental processes in filamentous fungi (W. Kim, unpublished). RNA modification, such as m⁶A, can be detected using direct RNA sequencing, whereby the modification sites can be profiled at nucleotide resolution (Leger et al., 2021). All these new discoveries using the Sordariomycetes models can be expected to evoke interest in exploring model fungal clades that can comprehensively illuminate these fundamental features.

The application of evolutionary approaches to genomic data from fungi may also help us to understand some impacts of climate change. Fungi are widely distributed and abundant in almost all ecosystems—even in extreme environments—and have been referred to as “climate warriors” in recognition of the important ecological roles that they play in the recycling of carbon, nitrogen, and other nutrients (Stajich, 2017; Averill et al., 2018; Tiquia-Arashiro and Grube, 2019; Pöggeler and James, 2023). Their presence and activity are considered to be useful indicators in relation to long-term climate change due to their sensitivity to surrounding conditions, such as changes in light, temperature, humidity, ROS elements, host type, and organic and inorganic pollution (Gadd et al., 2007; Frankland et al., 2009; Rodriguez-Romero et al., 2010). Several studies have reported on the impacts of climate change on fungus–host interactions, fungal distribution, fungal disease prevalence, and the production of fungal products (Frankland et al., 2009; Merrild, 2013; Botana and Sainz, 2015; Tiquia-Arashiro and Grube, 2019; Charters, 2020; Meyer et al., 2020; Frías-De-León et al., 2022; Miranda-Apodaca et al., 2023). The wide distribution and ecological diversity of Sordariomycetes fungi contributes to their frequent appearances in reports on the impact of climate change on fungal diversity, which occur especially frequently in climate-sensitive regions or populations of organisms that are closely associated with fungi.

Fungal pathogens that infect economically important crops, such as species of Fusarium (Vaughan et al., 2016) and Magnaporthe (Qiu et al., 2022), are of special concern. Epidemics of fungal pathogens can be enhanced by particularly wet and warm environments occurring during the flowering seasons of some crops. Remote sensing/geographic information system (GIS) technology has the potential to monitor snowline elevation, average temperature, precipitation, and sunshine hours in terms of their relationship with the product of Cordyceps sinensis (syn. Ophiocordyceps sinensis), which is also known as “yartsa gunbu” or “Dong Chong Xia Cao” (“winter worm summer grass”) in traditional Tibetan and Chinese medicine (Zhu et al., 2017). A comprehensive collection dataset and an ensemble species distribution modeling method have recently been used to investigate whether and how climate change affects the distribution of C. sinensis, and to predict potential shifts in the range of the fungus in the medium term of approximately 50–70 years in response to climate change (Yan et al., 2017; Li et al., 2019b). It has also been proposed that Trichoderma spp. could be utilized as “plant savers” in the face of climate change, on the basis of their several traits and genes that confer beneficial effects on crop plants (Kashyap et al., 2017). A limitation of these studies—with regard to their potential as a basis for omics-based analyses—is that they have thus far mainly addressed the ecological and diversity aspects of the global ecosystem. Hence, substantial fungal genomic resources that may illuminate potential responses to climate change have yet to be identified.

This would be a timely moment to revisit the possibility of developing N. discreta, along with other Sordariomycetes, as a model species to test the idea that adaptation to warm temperatures could lead to more efficient carbon metabolism (Romero-Olivares et al., 2015). To best adapt to their environments (often microenvironments), fungi have evolved elegant mechanisms for sensing and quickly responding to changes, and some of their genetic elements may be capable of high rates of evolution (e.g., Wang et al., 2016c; Chandra Nayaka et al., 2021; Kusch et al., 2023). Given the ecological and phenotypic diversity among closely related lineages within Sordariomycetes, further study and comparison of their potential for rapid genomic evolution would clarify their potential roles as models to enhance our understanding of long- and short-term climate and environmental impacts on fungi, and associated plant and animal health. As a motivating example, the relative abundance of Fusarium spp. has risen almost fivefold alongside the course of global warming (Delgado-Baquerizo et al., 2020).

We have only reviewed a very small portion of the recent comparative genomics and transcriptomics literature focusing on members of the class of Sordariomycetes, but these clearly illustrate the potential scientific rewards of comparing multiple genomes in different experimental settings to understand the evolution of the relevant organisms or traits and the genetics of select biological or ecological phenomena. However, the insights obtained on the basis of genomics/transcriptomics into trait evolution and into the associations with the genetics of various traits are still far from complete. Two possible factors that may significantly contribute to this gap are our underdeveloped understanding of the evolution of gene expression, and our lack of a system for integrating data from trait evolution and genetics that have already been (and can now be) intensively studied. Therefore, a large system encompassing well-studied model species, such as the Sordariomycetes, is a promising platform for the development of tools and the implementation of strategies to develop a systematic genetic understanding of trait evolution.