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Fig. 3 | Genome Biology

Fig. 3

From: Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC

Fig. 3

Recovery of MAGs belonging to Malassezia. We assembled 3910 metagenomes and could recover almost complete MAGs of M. globosa, M. restricta, M. sp., M. sloofiae and M. sympholidalis. Additionally, we recovered a Malassezia MAG with no known matching species. a Using four genes occurring in single copy in all representative Malassezia species, in the recovered MAGs as well as in S. cerevisiae and two species of Basidiomycota, we constructed a phylogenetic tree with MAFFT and FastTree2. The tree recapitulates the clustering suggested by Wu et al. [26], consisting of three clusters A, B and C. All recovered MAGs cluster next or close to their assigned species (bold). The MAG representing the unknown species (‘Novel_Malassezia_MAG’) is clustered within the Malassezia clade, confirming the previous annotation. b For each MAG, we counted the Reads Per Kilobase of transcript per Million mapped reads (RPKM) if more than 30% of the genome was present in a sample. Using this approach, we could detect M. globosa, M. restricta and M. sp. across all individual subjects. The less prevalent M. sloofiae and M. sympholidalis could only be found in 2 and 6 individuals, respectively. The ‘Novel_Malassezia_MAG’ could be found in four subjects. c We analysed the MAG using anvi’o’s refine method. All clusters created by anvi’o based on k-mer frequency and coverage have similar coverage and could be annotated as Malassezia using UniRef90. Cluster E has a lower GC content but comparable coverage to other clusters

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