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Figure 6 | Genome Biology

Figure 6

From: The genome sequence of the model ascomycete fungus Podospora anserina

Figure 6

Gene gain and loss in fungal genomes. (a-c) Unrooted phylogenetic trees of putative alkaline phosphatase D precusors (a), putative HC-toxin efflux carrier proteins related to ToXA from Cochliobolus carbonum (b), and putative chitinases related to the killer toxin of Kluyveromyces lactis (c). The putative CDSs were aligned with ProbCons 1.10 [101] and manually edited to eliminate poorly conserved regions, resulting in alignment over 565, 544, 505 amino acids, respectively. Phylogenetic trees were constructed with Phyml 2.4.4 [102] under the WAG model of amino acid substitution. The proportion of variable sites and the gamma distribution parameters of four categories of substitution rate were estimated by phyml. For each tree, we performed 100 boostrap replicates. The recently duplicated P. anserina paralogues are highlighted in red and the divergent duplication of chitinases in green. Trees with similar topologies and statistical support (1,000 boostrap replicates) were recovered with the neighbor joining method. Especially, recent duplication of Pa_4_1520/Pa_6_8120, Pa_2_7900/Pa_6_8600 and Pa_4_5560/Pa_5_1570 as well as the distinction of the two subfamilies of chitinases were recovered with 100% confidence. AN, A. nidulans; MGG, M. grisea; NC, N. crassa; Pa, P. anserina.

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