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De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Figure 4

Phylogenetic analysis and expression of genes from different orthogroups from an OrthoMCL analysis of S. macrospora (SM), N. crassa (NC), N. discreta (ND), C. globosum (CHG), and P. anserina (PA).

(A) Species phylogeny with six concatenated genes that are single-copy orthologs in each of the five species. (B–E) Phylogenetic trees with five different orthogroups. Outgroups for the trees were homologs from either Nectria haematococca, Aspergillus fumigatus, Penicillium chrysogenum, or Pyrenophora tritici-repentis. Numbers at branches indicate bootstrap support (10,000 bootstrap replications) in % for neighbor joining trees. (D–E) Expression of the S. macrospora and N. crassa genes from orthogroups 49 and 180 during sexual development compared to vegetative growth. Expression data are the results of two independent experiments and were determined by quantitative real time PCR. The red and green dashed lines indicate two-fold up- and downregulation, respectively. n.e., no expression was detected during vegetative growth or sexual development.

Figure 4