A genome-scale phylogeny of the kingdom Fungi

Li, Yuanning; Steenwyk, Jacob L.; Chang, Ying; Wang, Yan; James, Timothy Y.; Stajich, Jason E.; Spatafora, Joseph W.; Groenewald, Marizeth; Dunn, Casey W.; Hittinger, Chris Todd; Shen, Xing‐Xing; Rokas, Antonis

doi:10.1016/j.cub.2021.01.074

Cited by 222 publications

(277 citation statements)

References 80 publications

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“…This requires a well-resolved phylogeny of fungi including all zoosporic lineages. Unfortunately, previous phylogenomic analyses did not resolve which zoosporic group, either Blastocladiomycota or Chytridiomycota, is sister to non-flagellated fungi 21,[26][27][28] . This lack of resolution may result from the old age of these splits (~0,5-1 Ga) 3,29,30 and the existence of several radiations of fungal groups, notably during their co-colonization of land with plants 25,31 , which would leave limited phylogenetic signal to resolve these deep nodes 22 .…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

Galindo

López‐García

Torruella

et al. 2020

Preprint

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Compared to well-known multicellular fungi and unicellular yeast, unicellular fungi with zoosporic, free-living flagellated stages remain poorly known and their phylogenetic position is often unresolved. Recently, 18S+28S rRNA gene molecular phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and record-long simplified kinetosomes, Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without affinity with any known fungal clade. To assess their phylogenetic position and unique trait evolution, we sequenced single-cell genomes for both species. Phylogenomic analyses using 264 protein markers and a comprehensive taxon sampling retrieved and almost fully-resolved fungal tree with these species forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Chytridiomycota branched as sister to all other fungi, and the zoosporic fungus Olpidium bornovanus as sister to non-flagellated fungi. Comparative genomic analyses across Holomycota revealed an atypically reduced metabolic repertoire for sanchytrids given their placement in the tree. We infer four independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. The highly reduced sanchytrid flagellar machinery, notably their long kinetosome, might have been retained to support a putative light-sensing lipid organelle. Together with their phylogenetic position, these unique traits justify the erection of the novel phylum Sanchytriomycota. Our results also show that most of the hyphal morphogenesis gene repertoire of multicellular Fungi had already evolved in early holomycotan lineages.

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Section: Introductionmentioning

confidence: 99%

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

Galindo

López‐García

Torruella

et al. 2020

Preprint

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“…Non-insect invertebrates and fungi, in particular, have seen few studies examining introgression given they represent a vast amount of biological and phylogenetic diversity. Given the extensive genome resources available for fungi (Stajich, et al 2012;Matute and Sepúlveda 2019;James, et al 2020;Li, et al 2021) and the abundance of verbal arguments that suggest that hybridization is one of the leading forces in fungal evolution (Nelson 1963;Steensels, et al 2021), the time is ripe to determine whether gene exchange is more prevalent in fungi than in other clades. Even within insects, most studies have occurred either in Dipterans or Lepidopterans, with few studies in other insect systems.…”

Section: Introgression Has Been Mostly Studied In Plants and Mammalsmentioning

confidence: 99%

15 years of introgression studies: quantifying gene flow across Eukaryotes

Peede

et al. 2021

Preprint

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With the rise of affordable next generation sequencing technology, introgression - or the exchange of genetic materials between taxa - is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Patterson's D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most-often used introgression statistic, Patterson's D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

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“…CC-BY 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted April 11, 2021. ; https://doi.org/10.1101/2021.04.09.439159 doi: bioRxiv preprint the relation is best described as a polytomy (Li et al, 2021). Interestingly, with the addition of a considerable number of AM fungal genomes presented in this study, we recover yet a new topology among the three sister lineages (Fig.…”

Section: Discussionmentioning

confidence: 58%

“…In the study Glomerales was recovered as polyphyletic (Beaudet et al, 2018), in contrast to earlier ribosomal genes phylogenies where Glomerales was found to be monophyletic (Krüger et al, 2012). Other phylogenomic studies have not adressed relations among families largelly due to limited taxon sampling (Sun et al, 2018;Morin et al, 2019, Venice et al, 2020, Li et al, 2021. Due to difficulties in obtaining enough pure DNA for whole genome sequencing available genomic data still represent only a fraction of the diversity of AM fungi.…”

Section: Introductionmentioning

confidence: 63%

“…Available literature identify that all AM fungi form a monophyletic lineage within the fungal kingdom. This lineage is taxonomically classified either as a phylum, Glomeromycota, (Schüβler, Schwarzott and Walker, 2001;James et al, 2006;Hibbett et al, 2007;Schüßler and Walker, 2010;Tedersoo et al, 2018) or as the sub-phylum Glomeromycotina, which together with Morteriellomycotina and Mucoromycotina, make up the phylum Mucoromycota (Spatafora et al, 2016;James et al, 2020, Li et al, 2021. The current consensus classification of AMfungal species into genera and families was established by Redecker and co-authors in 2013, when systematists with long experience in the biology and taxonomy of AM fungi joined forces .…”

Section: Introductionmentioning

confidence: 99%

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In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

Montoliu-Nerin

Sánchez‐García

Bergin

et al. 2021

Preprint

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Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the phylogeny and evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates high-quality genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. Based on analyses of sets of orthologous genes, we highlight three alternative topologies among families of AM fungi. In the main topology, Glomerales is polyphyletic and Claroideoglomeraceae, is the basal sister group to Glomeraceae and Diversisporales. Our results support family level classification from previous phylogenetic studies. New evolutionary relationships among families where highlighted with phylogenomic analysis using the hitherto most extensive taxon sampling for AM fungi.

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A genome-scale phylogeny of the kingdom Fungi

Cited by 222 publications

References 80 publications

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

15 years of introgression studies: quantifying gene flow across Eukaryotes

In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

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