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Fig. 6 | BMC Evolutionary Biology

Fig. 6

From: Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose

Fig. 6

The inferred evolutionary history of the Ceratocystidaceae Glycoside hydrolase 32 (GH32) gene family and the orthology relationships among these genes. a The evolutionary tree shows nine homologous genes from six species (A). The Huntiella cell wall invertase genes are depicted as HsINV-CW, HmINV-CW and HoINV-CW, while the Ceratocystis vacuolar invertase genes are depicted as CaINV-V, CmINV-V and CfINV-V and those encoding the Ceratocystis cell wall invertases as CaINV-CW, CmINV-CW and CfINV-CW. As indicated by CAFE, the genome of the Ceratocystidaceae ancestor likely encoded two invertase (INV) genes, one of which (depicted by the grey line) was subsequently lost from both the Ceratocystis and Huntiella lineages (depicted by grey broken line) before the radiation of species. However, the remaining invertase gene (depicted in orange) was duplicated in the Ceratocystis ancestor resulting in the two invertase genes encoded by the genomes of the extant species. This duplication was also reconstructed using NOTUNG 2.6 which detects duplications based on gene tree to species tree reconciliation [89] (results not shown). All of the invertase genes in the extant Ceratocystis and Huntiella species thus evolved from the same ancestral gene in the Ceratocystidaceae ancestor (depicted by the orange line). The respective Ceratocystis genes each evolved through vertical decent after their emergence (i.e., gene duplication) in the last common ancestor. b Following the standard nomenclature for duplicated genes (reviewed by Koonin [36]), the Huntiella cell wall invertase genes share an orthologous relationship (i.e., orthologs are related via speciation and are derived via vertical decent from the common ancestor). The same is also true for the respective cell wall and vacuolar invertase genes of Ceratocystis, where each represent a set of orthologs. Because the duplication that gave rise to the Certocystis genes occurred before radiation of this genus, the Ceratocystis cell wall and vacuolar invertase genes represent outparalogs (i.e., homologs that derive from a gene duplication event that precedes lineage radiation/speciation) [36]. However, all of the Ceratocysistis invertase genes represent co-orthologs of the gene in Huntiella. This is because the lineage-specific duplication in Ceratocystis gave rise to a set of genes that are collectively orthologous to those of Huntiella [36]

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