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Banchi E, Manna V, Muggia L, Celussi M. Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea). MICROBIAL ECOLOGY 2024; 87:78. [PMID: 38806848 DOI: 10.1007/s00248-024-02394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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2
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Vargas-Gastélum L, Romer AS, Ghotbi M, Dallas JW, Alexander NR, Moe KC, McPhail KL, Neuhaus GF, Shadmani L, Spatafora JW, Stajich JE, Tabima JF, Walker DM. Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria. mSphere 2024; 9:e0047523. [PMID: 38349154 PMCID: PMC10964425 DOI: 10.1128/msphere.00475-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/10/2024] [Indexed: 03/27/2024] Open
Abstract
Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexander S. Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Marjan Ghotbi
- Research Division 3, Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jason W. Dallas
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - N. Reed Alexander
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kylie C. Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - George F. Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Leila Shadmani
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Javier F. Tabima
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Donald M. Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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3
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Iizuka R, Hattori S, Kosaka Y, Masaki Y, Kawano Y, Ohtsu I, Hibbett D, Katayama Y, Yoshida M. Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum. Appl Environ Microbiol 2024; 90:e0201523. [PMID: 38299812 PMCID: PMC10880591 DOI: 10.1128/aem.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is clade D of the β-class carbonic anhydrase subfamily enzyme with high specificity for COS but low activity for CO2 hydration, showed that the COSase is involved in COS assimilation. Comparison of sulfur metabolites of strain THIF08 revealed a higher relative abundance of reduced sulfur compounds under the COS-supplemented condition than the sulfate-supplemented condition, suggesting that sulfur assimilation is more energetically efficient with COS than with sulfate because there is no redox change of sulfur. Phylogenetic analysis of the genes encoding COSase, which are distributed in a wide range of fungal taxa, suggests that the common ancestor of Ascomycota, Basidiomycota, and Mucoromycota acquired COSase at about 790-670 Ma.IMPORTANCEThe biological assimilation of gaseous CO2 and N2 involves essential processes known as carbon fixation and nitrogen fixation, respectively. In this study, we found that the fungus Trichoderma harzianum strain THIF08 can grow with gaseous carbonyl sulfide (COS), the most abundant and ubiquitous gaseous sulfur compound, as a sulfur source. When the fungus grew in these conditions, COS was assimilated into sulfur metabolites, and the key enzyme of this assimilation process is COS hydrolase (COSase), which specifically degrades COS. Moreover, the pathway was more energy efficient than the typical sulfate assimilation pathway. COSase genes are widely distributed in Ascomycota, Basidiomycota, and Mucoromycota and also occur in some Chytridiomycota, indicating that COS assimilation is widespread in fungi. Phylogenetic analysis of these genes revealed that the acquisition of COSase in filamentous fungi was estimated to have occurred at about 790-670 Ma, around the time that filamentous fungi transitioned to a terrestrial environment.
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Affiliation(s)
- Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shohei Hattori
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu, China
| | - Yusuke Kosaka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yusuke Kawano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - Iwao Ohtsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - David Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties, Taito-ku, Tokyo, Japan
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Rúa-Giraldo ÁL. Fungal taxonomy: A puzzle with many missing pieces. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:288-311. [PMID: 37721899 PMCID: PMC10588969 DOI: 10.7705/biomedica.7052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.
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Seto K, Simmons DR, Quandt CA, Frenken T, Dirks AC, Clemons RA, McKindles KM, McKay RML, James TY. A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. mBio 2023; 14:e0131323. [PMID: 37486265 PMCID: PMC10470594 DOI: 10.1128/mbio.01313-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.
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Affiliation(s)
- Kensuke Seto
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - D. Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Cluster Nature and Society, HAS University of Applied Sciences, 's-Hertogenbosch, the Netherlands
| | - Alden C. Dirks
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rebecca A. Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Katelyn M. McKindles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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6
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Merényi Z, Krizsán K, Sahu N, Liu XB, Bálint B, Stajich JE, Spatafora JW, Nagy LG. Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits. Nat Ecol Evol 2023; 7:1221-1231. [PMID: 37349567 PMCID: PMC10406608 DOI: 10.1038/s41559-023-02095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - Neha Sahu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Jason E Stajich
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary.
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Tubulin Polymerization Promoting Proteins (TPPPs) of Aphelidiomycota: Correlation between the Incidence of p25alpha Domain and the Eukaryotic Flagellum. J Fungi (Basel) 2023; 9:jof9030376. [PMID: 36983544 PMCID: PMC10057920 DOI: 10.3390/jof9030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The seven most early diverging lineages of the 18 phyla of fungi are the non-terrestrial fungi, which reproduce through motile flagellated zoospores. There are genes/proteins that are present only in organisms with flagellum or cilium. It was suggested that TPPP-like proteins (proteins containing at least one complete or partial p25alpha domain) are among them, and a correlation between the incidence of the p25alpha domain and the eukaryotic flagellum was hypothesized. Of the seven phyla of flagellated fungi, six have been known to contain TPPP-like proteins. Aphelidiomycota, one of the early-branching phyla, has some species (e.g., Paraphelidium tribonematis) that retain the flagellum, whereas the Amoeboaphelidium genus has lost the flagellum. The first two Aphelidiomycota genomes (Amoeboaphelidium protococcorum and Amoeboaphelidium occidentale) were sequenced and published last year. A BLASTP search revealed that A. occidentale does not have a TPPP, but A. protococcorum, which possesses pseudocilium, does have a TPPP. This TPPP is the ‘long-type’ which occurs mostly in animals as well as other Opisthokonta. P. tribonematis has a ‘fungal-type’ TPPP, which is found only in some flagellated fungi. These data on Aphelidiomycota TPPP proteins strengthen the correlation between the incidence of p25alpha domain-containing proteins and that of the eukaryotic flagellum/cilium.
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9
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On the TPPP Protein of the Enigmatic Fungus, Olpidium-Correlation between the Incidence of p25alpha Domain and That of the Eukaryotic Flagellum. Int J Mol Sci 2022; 23:ijms232213927. [PMID: 36430412 PMCID: PMC9698843 DOI: 10.3390/ijms232213927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Loss of the flagellum was an important step in the evolution of fungi. The flagellated fungi of the phylum Olpidiomycota are the closest relative of the non-flagellated terrestrial fungi. There are genes encoding proteins, the occurrence of which shows a strong correlation with the incidence of the flagellum. One of these gene/protein families is "TPPP-like proteins" whose main feature is the presence of the p25alpha domain. The functional link between TPPP and flagellum has also been shown. Most of the phyla of flagellated fungi have been known to contain TPPP-like proteins but Olpidiomycota was an exception. This study demonstrates that Olpidium bornovanus, similarly to some fungi of Chytridiomycota and Blastocladiomycota, has a "fungal-type" TPPP characterized by the presence of two (a complete and an incomplete) p25alpha domains.
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10
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Smith TJ, Donoghue PCJ. Evolution of fungal phenotypic disparity. Nat Ecol Evol 2022; 6:1489-1500. [PMID: 35970862 DOI: 10.1038/s41559-022-01844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated; zygomycetous; sac-bearing; and club-bearing. The discontinuity between morphotypes is a consequence of extinction, indicating that a complete record of fungal disparity would present a more homogeneous distribution of form. Fungal disparity expands episodically through time, punctuated by a sharp increase associated with the emergence of multicellular body plans. Simulations show these temporal trends to be non-random and at least partially shaped by hierarchical contingency. These trends are decoupled from changes in gene number, genome size and taxonomic diversity. Only differences in organismal complexity, characterized as the number of traits that constitute an organism, exhibit a meaningful relationship with fungal disparity. Both animals and fungi exhibit episodic increases in disparity through time, resulting in distributions of form made discontinuous by extinction. These congruences suggest a common mode of multicellular body plan evolution.
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Affiliation(s)
- Thomas J Smith
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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11
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Abstract
It has been assumed that fungi are characterized by a haploid-dominant life cycle with a general absence of mitosis in the diploid stage (haplontic life cycles). However, this characterization is based largely on information for Dikarya, a group of fungi that contains mushrooms, lichens, molds, yeasts, and most described fungi. We now appreciate that most early-diverging lineages of fungi are not Dikarya and share traits with protists, such as flagellated life stages. Here, we generated an improved phylogeny of the fungi by generating genome sequences of 69 zoosporic fungi. We show, using the estimated heterozygosity of these genomes, that many fungal lineages have diploid-dominant life cycles (diplontic). This finding forces us to rethink the early evolution of the fungal cell. Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane– and cell-wall–associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.
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12
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Chang Y, Wang Y, Mondo S, Ahrendt S, Andreopoulos W, Barry K, Beard J, Benny GL, Blankenship S, Bonito G, Cuomo C, Desiro A, Gervers KA, Hundley H, Kuo A, LaButti K, Lang BF, Lipzen A, O’Donnell K, Pangilinan J, Reynolds N, Sandor L, Smith ME, Tsang A, Grigoriev IV, Stajich JE, Spatafora JW. Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies. iScience 2022; 25:104840. [PMID: 35996588 PMCID: PMC9391592 DOI: 10.1016/j.isci.2022.104840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition. Our analyses revealed that phylogeny played an important role in shaping the secretome composition of zygomycete fungi with trophic mode contributing a smaller amount. Reconstruction of the evolution of secreted digestive enzymes revealed lineage-specific expansions, indicating that Mucoromycota and Zoopagomycota followed different trajectories early in their evolutionary history. We identified the presence of multiple pathogenicity-related proteins in the lineages known as saprotrophs, suggesting that either the ecologies of these fungi are incompletely known, and/or that these pathogenicity-related proteins have important functions associated with saprotrophic ecologies, both of which invite further investigation.
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Affiliation(s)
- Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Stephen Mondo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Jeff Beard
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Gerald L. Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Sabrina Blankenship
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Gregory Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Alessandro Desiro
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Kyle A. Gervers
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Hope Hundley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - B. Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kerry O’Donnell
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Nicole Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Laura Sandor
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Matthew E. Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Igor V. Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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13
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Strassert JFH, Monaghan MT. Phylogenomic insights into the early diversification of fungi. Curr Biol 2022; 32:3628-3635.e3. [PMID: 35830854 DOI: 10.1016/j.cub.2022.06.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022]
Abstract
Phylogenomic analyses have boosted our understanding of the evolutionary trajectories of all living forms by providing continuous improvements to the tree of life.1-5 Within this tree, fungi represent an ancient eukaryote group,6 having diverged from the animals ∼1.35 billion years ago.7 Estimates of the number of extant species range between 1.5 and 3.8 million.8,9 Recent reclassifications and the discovery of the deep-branching Sanchytriomycota lineage10 have brought the number of proposed phyla to 20,11 21 if the Microsporidia are included.12-14 Uncovering how the diverse and globally distributed fungi are related to each other is fundamental for understanding how their lifestyles, morphologies, and metabolic capacities evolved. To date, many of the proposed relationships among the phyla remain controversial and no phylogenomic study has examined the entire fungal tree using a taxonomically comprehensive dataset and suitable models of evolution. We assembled and curated a 299-protein dataset with a taxon sampling broad enough to encompass all recognized fungal diversity with available data, but selective enough to run computationally intensive analyses using best-fitting models. Using a range of reconstruction methods, we were able to resolve many contested nodes, such as a sister relationship of Chytridiomyceta to all other non-Opisthosporidia fungi (with Chytridiomycota being sister to Monoblepharomycota + Neocallimastigomycota), a branching of Blastocladiomycota + Sanchytriomycota after the Chytridiomyceta but before other non-Opisthosporidia fungi, and a branching of Glomeromycota as sister to the Dikarya. Our up-to-date fungal tree of life will serve as a springboard for future investigations on the early evolution of fungi.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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14
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Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
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Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
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15
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Liimatainen K, Kim JT, Pokorny L, Kirk PM, Dentinger B, Niskanen T. Taming the beast: a revised classification of Cortinariaceae based on genomic data. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00499-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AbstractFamily Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
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16
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Corsaro D. Insights into Microsporidia Evolution from Early Diverging Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:71-90. [PMID: 35543999 DOI: 10.1007/978-3-030-93306-7_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microsporidia have drastically modified genomes and cytology resulting from their high level of adaptation to intracytoplasmic parasitism. Their origins, which had long remained enigmatic, were placed within the line of Rozella, a primitive endoparasitic chytrid. These origins became more and more refined with the discovery of various parasites morphologically similar to the primitive lines of microsporidia (Metchnikovellids and Chytridiopsids) but which possess fungal-like genomes and functional mitochondria. These various parasites turn out to be distinct missing links between a large assemblage of chytrid-like rozellids and the true microsporidians, which are actually a very evolved branch of the rozellids themselves. The question of how to consider the historically known Microsporidia and the various microsporidia-like organisms within paraphyletic rozellids is discussed.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS Chlamydia Research Association, Vandoeuvre-lès-Nancy, France.
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17
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Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals. FUNGAL DIVERS 2021; 109:59-98. [PMID: 34608378 PMCID: PMC8480134 DOI: 10.1007/s13225-021-00480-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/19/2021] [Indexed: 01/02/2023]
Abstract
The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.
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18
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Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Curr Biol 2021; 31:1653-1665.e5. [PMID: 33607033 PMCID: PMC8347878 DOI: 10.1016/j.cub.2021.01.074] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 12/22/2022]
Abstract
Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Department of Biological Sciences, University of Toronto Scarborough and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, 3584 CT, Utrecht 85167, the Netherlands
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xing-Xing Shen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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19
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Žárský J, Žárský V, Hanáček M, Žárský V. Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split. FRONTIERS IN PLANT SCIENCE 2021; 12:735020. [PMID: 35154170 PMCID: PMC8829067 DOI: 10.3389/fpls.2021.735020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/17/2021] [Indexed: 05/05/2023]
Abstract
For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.
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Affiliation(s)
- Jakub Žárský
- CryoEco Research Group, Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Jakub Žárský,
| | - Vojtěch Žárský
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Martin Hanáček
- Polar-Geo-Lab, Department of Geography, Faculty of Science, Masaryk University, Brno, Czechia
- Regional Museum in Jeseník, Jeseník, Czechia
| | - Viktor Žárský
- Laboratory of Cell Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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