De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis
(A) Region from S. macrospora scaffold 98 and N. crassa contig 8 containing het-c and pin-c genes. A syntenic region containing the N. crassa het-c and pin-c genes and the orthologous region in S. macrospora is shaded in blue. In S. macrospora, this region is bordered by additional copies of pin-c and a partial het-c (left) and a TOL-related protein encoding gene (right). The tol-related gene SMAC_07228 contains an internal stop codon within the open reading frame (indicated by an asterisk) and therefore encodes a shortened TOL-related protein or is a pseudogene. (B) Phylogenetic tree of PIN-C and TOL-related proteins from the genomic region shown in (A). For N. crassa, three allelic variations of PIN-C (PIN-C1, PIN-C2, and PIN-C3) were used for tree construction. The PIN-C1 protein from Pyrenophora tritici-repentis was used as an outgroup to root the tree. Maximum parsimony and neighbor joining trees were calculated with 10,000 bootstrap replications each. The phylogenetic tree separates the PIN-C and TOL-related proteins, however, it is not conclusive with respect to the putative ancestral state of the PIN-C alleles.