Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets

Nagy, László G.; Szöllősi, Gergely J.

doi:10.1016/bs.adgen.2017.09.008

Cited by 17 publications

(13 citation statements)

References 74 publications

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“…First , this gene family is present in all the major fungal groups from the most primitive to the most recently evolved. Interestingly, CLO/PXG -like sequences are present in the two basal clades, Microsporidia and Cryptomycota, which have only very recently (and, to date, not unanimously) been accepted as likely members of the Fungi [89–94]. Second , the CLO/PXG-like protein sequences are generally well conserved and their major canonical motifs (see below) are strikingly similar to orthologs that are highly abundant in the Viridiplantae [4].…”

Section: Discussionmentioning

confidence: 99%

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

et al. 2018

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BackgroundCaleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim of this study was to investigate the evolution and functions of the CLO/PXGs in the Fungi and other non-plant clades and to elucidate the overall origin of this gene family.ResultsCLO/PXG-like genes are distributed across the full range of fungal groups from the basal clades, Cryptomycota and Microsporidia, to the largest and most complex Dikarya species. However, the genes were only present in 243 out of 844 analysed fungal genomes. CLO/PXG-like genes have been retained in many pathogenic or parasitic fungi that have undergone considerable genomic and structural simplification, indicating that they have important functions in these species. Structural and functional analyses demonstrate that CLO/PXGs are multifunctional proteins closely related to similar proteins found in all major taxa of the Chlorophyte Division of the Viridiplantae. Transcriptome and physiological data show that fungal CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression and are upregulated in response to a range of biotic and abiotic stresses as well as participating in key metabolic and developmental processes such as lipid metabolism, signalling, reproduction and pathogenesis. Biochemical data also reveal that the Aspergillus flavus CLO/PXG has specific functions in sporulation and aflatoxin production as well as playing roles in lipid droplet function.ConclusionsIn contrast to plants, CLO/PXGs only occur in about 30% of sequenced fungal genomes but are present in all major taxa. Fungal CLO/PXGs have similar but not identical roles to those in plants, including stress-related oxylipin signalling, lipid metabolism, reproduction and pathogenesis. While the presence of CLO/PXG orthologs in all plant genomes sequenced to date would suggest that they have core housekeeping functions in plants, the selective loss of CLO/PXGs in many fungal genomes suggests more restricted functions in fungi as accessory genes useful in particular environments or niches. We suggest an ancient origin of CLO/PXG-like genes in the ‘last eukaryotic common ancestor’ (LECA) and their subsequent loss in ancestors of the Metazoa, after the latter had diverged from the ancestral fungal lineage.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5334-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

et al. 2018

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“…To better understand the evolution of species diversity and ecological lifestyles in the Ascomycota, a robust framework of phylogenetic relationships and divergence time estimates is essential (9)(10)(11). In the last two decades, several studies have aimed to infer the phylogeny of the Ascomycota either using a handful of gene markers from hundreds of taxa (12)(13)(14)(15)(16) or using hundreds of gene markers from tens of taxa (17)(18)(19)(20). To date, the most comprehensive "few-markers-from-many-taxa" phylogeny used a 6-gene, 420-taxon (8 Taphrinomycotina, 1 6 Saccharomycotina, and 396 Pezizomycotina) data matrix (12), whereas the most comprehensive genome-scale phylogeny used a 238-gene, 496-taxon (12 Taphrinomycotina, 76 Saccharomycotina, and 408 Pezizomycotina) data matrix (21) but was inferred using FastTree, a program that is faster but typically yields phylogenies that have much lower likelihood scores than those obtained by IQ-TREE and RAxML/RAxML-NG (22).…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, relationships among classes are contentious between studies, particularly with respect to relationships between the 16 classes in Pezizomycotina ( 1 ). For example, there is disagreement whether the sister group to the rest of classes in the Pezizomycotina is class Pezizomycetes ( 13 ), class Orbiliomycetes ( 16 ), or a clade composed of both ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

et al. 2020

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Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

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“…There are more than 30,000 species in Basidiomycota, and this number is increasing day by day [4]. More specifically, this division of characterization can be portrayed under the number of request of gilled and nongilled fungi [5].…”

Section: Basidiomycetesmentioning

confidence: 99%

Importance of Molecular and Phylogenetic Analyses for Identification of Basidiomycetes

Sarwar¹,

Firdous²,

Khalid³

2019

Recent Advances in Phylogenetics

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Fungi are considered as diverse group of eukaryotic organisms and have very important role in ecosystem. Although their expected number is more than 2.2-3.8 million, only 120,000 taxa have been identified so far. Basidiomycetes are very large group of fungi including mushrooms, toad stools, puff balls, earth stars, polypores, and rust and smut fungi. Previously, these fungi were identified only by morphological characters that have been considered as variable due to environmental factors. Literature shows that many fungi are misidentified due to phenotypic changes. Molecular methods including phylogenetics prove to be successful aids along with traditional methods for correct identification of these fungi and these have revolutionized fungal reclassification. Many fungal taxa have been shifted to other groups of fungi after their phylogenetic analysis. So, many DNA markers can be used to solve such problems.

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Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets

Cited by 17 publications

References 74 publications

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Importance of Molecular and Phylogenetic Analyses for Identification of Basidiomycetes

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