Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

AbstractParmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

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Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data

Molecular Cell ◽

10.1016/s1097-2765(02)00531-2 ◽

2002 ◽

Vol 9 (5) ◽

pp. 1133-1143 ◽

Cited By ~ 136

Author(s):

Patrick Kemmeren ◽

Nynke L. van Berkum ◽

Jaak Vilo ◽

Theo Bijma ◽

Rogier Donders ◽

...

Keyword(s):

Protein Interaction ◽

Functional Annotation ◽

Integrated Analysis ◽

Genome Scale ◽

Scale Data

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Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

PLoS ONE ◽

10.1371/journal.pone.0053930 ◽

2013 ◽

Vol 8 (1) ◽

pp. e53930 ◽

Cited By ~ 2

Author(s):

Julia Salzman ◽

Daniel M. Klass ◽

Patrick O. Brown

Keyword(s):

Molecular Interactions ◽

Adaptive Model ◽

Model Based ◽

Genome Scale ◽

Scale Data

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Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽

10.1186/s43008-019-0018-2 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Claudio G. Ametrano ◽

Felix Grewe ◽

Pedro W. Crous ◽

Stephen B. Goodwin ◽

Chen Liang ◽

...

Keyword(s):

Character State ◽

Ancestral Character State ◽

Wide Range ◽

Tree Inference ◽

Ancestral Character State Reconstruction ◽

Inference Methods ◽

Genome Scale ◽

The Impact ◽

Rock Inhabiting Fungi ◽

Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

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