Phylogenetic analysis of Hypocreales species based on concatenated nucleotide sequences of 14 typical mitochondrial PCGs. The tree shown here is the single best topology recovered from ML. Support values (ML/BI) are indicated for nodes if they receive posterior probability < 0.95 (for BI) or bootstrap values < 70% (for ML). Clades of Akanthomyces, Beauveria, and Cordyceps are highlighted because each of these genera contains more than two species without taxonomic ambiguity

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... of nad4 (Additional file 1: Table S4). Although local BLASTN searches failed to support the splicing of the nad4 intron (nad4P505), RT-PCR confirmed the excision of the nad4 intron (Additional file 2: Fig. S5). The splicing of the nad4 intron was also supported by local BLASTN searches against de novo assembled transcripts (Additional file 2: Fig. ...

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... phylogeny-building methods (BI & ML) generated identical topologies. Phylogenetic trees constructed by different datasets (DNA & protein), however, showed topological differences ( Fig. 6; Additional file 2: Fig. S7). For instance, Tolypocladium inflatum grouped together with two other Ophiocordycipitaceae species at a low support (55% ML) in the DNA tree, whereas the three species failed to group together in the protein tree. Besides, fungal species of every family clustered together with high support values (Fig. 6). ...

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... differences ( Fig. 6; Additional file 2: Fig. S7). For instance, Tolypocladium inflatum grouped together with two other Ophiocordycipitaceae species at a low support (55% ML) in the DNA tree, whereas the three species failed to group together in the protein tree. Besides, fungal species of every family clustered together with high support values (Fig. 6). Phylogenetic Table S2 for details of the FPKM values. Please note that the free-standing genes atp8 and all trn genes, and the intronic ORF orf112 have a FPKM value of zero, and thus they are not shown in the figure Fig. 4 Comparison between the C. blackwelliae mitogenome and the assembled transcripts. (A) BLASTN analysis of the ...

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... exon cannot be shown by the genome comparison visualizer Easyfig, and hence we artificially add a brown line to indicate the position of the exon. By this way, all introns except nad4P505 are seen to be excised Zhang et al. IMA Fungus (2023) 14:13 relationship among different families also showed subtle differences between DNA and protein trees ( Fig. 6; Additional file 2: Fig. S7). Although these variations, C. blackwelliae always clustered into the Cordycipitaceae clade, being closely related to C. chanhua with a high support (98% in DNA tree and 80% in protein ...

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... to date. There are currently 14 accepted families in Hypocreales ( Hyde et al. 2020), and other six families (i.e., Calcarisporiaceae, Cocoonihabitaceae, Flammocladiellaceae, Myrotheciomycetaceae, Niessliaceae, and Tilachlidiaceae) still lack available mitogenomes. As expected, C. blackwelliae clustered into the Cordycipitaceae clade ( Fig. 6; Additional file 2: Fig. S7). Cordycipitaceae species with available mitogenomes are from the following seven genera: Akanthomyces, Beauveria, Cordyceps, Isaria, Lecanicillium, Parengyodontium, and Samsoniella. For three of these genera, Akanthomyces, Beauveria, and Cordyceps, each contained more than two species in our study, and ...

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... species with available mitogenomes are from the following seven genera: Akanthomyces, Beauveria, Cordyceps, Isaria, Lecanicillium, Parengyodontium, and Samsoniella. For three of these genera, Akanthomyces, Beauveria, and Cordyceps, each contained more than two species in our study, and fungal taxa from each of these genera grouped together (Fig. 6). Two Lecanicillium species (Lecanicillium saksenae and Lecanicillium fungicola) were also employed in this study, but they did not cluster together (Fig. 6). This is consistent to the polyphyly of Lecanicillium and the suggested suppression of this generic name in Cordycipitaceae ( Kepler et al. 2017). Actually, several species ...

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... Samsoniella. For three of these genera, Akanthomyces, Beauveria, and Cordyceps, each contained more than two species in our study, and fungal taxa from each of these genera grouped together (Fig. 6). Two Lecanicillium species (Lecanicillium saksenae and Lecanicillium fungicola) were also employed in this study, but they did not cluster together (Fig. 6). This is consistent to the polyphyly of Lecanicillium and the suggested suppression of this generic name in Cordycipitaceae ( Kepler et al. 2017). Actually, several species previously placed in Lecanicillium have been transferred into other genera, including Akanthomyces, Flavocillium, and Gamszarea (Kepler et al. 2017;Wang et al. ...