Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2012
Publication Date: 5/22/2012
Publication URL: http://dx.doi.org/10.1016/j.ympev.2012.05.005
Citation: Walker, D., Castlebury, L.A., Rossman, A.Y., White, J. 2012. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota). Molecular Phylogenetics and Evolution. 64:500-512. Interpretive Summary: Fungi are an important group of organisms that cause serious damage to many agricultural and forest resources. Within a group of canker-causing fungi it is often difficult to identify species based on the appearance of the organism, thus molecular sequences of specific genes are used for this purpose. However, the number of genes that are used to define species is limited. In this research entire genomes were compared to discover new genes that might be useful. Two genes were found that were determined to correlate with previously defined species. Sequences of the new genes can be combined with the previously used genes to determine the relationships of these species. These new genes also proved to be useful for the identification of many other fungi. This research will be used by plant pathologists who need to accurately define species in order to develop diagnostic techniques for the rapid identification of disease-causing fungi.
Technical Abstract: Although significant progress has been made resolving deep branches of the fungal tree of life in recent works, many fungal systematists are interested in species-level questions to both define species and to assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers to better represent the whole genome. We report universal ascomycete primers for two newly identified single copy protein coding genes, FG1093 and MS204. Phylogenetic utility was tested in two genera Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). We compared the phylogenetic performance of ß-tubulin, the ITS region including ITS1, 5.8S rDNA and ITS2, and tef-la with FG1093 and MS204. We found that phylogenies inferred from FG1093 and MS204 were largely in agreement with ß-tubulin, ITS, and tef-1a although some topological conflict was observed in Ophiognomonia when comparing ß-tubulin and FG1093 to the other genes. The combination of genes that yielded the best resolution and support were different for each genus. Based on two separate tests of phylogenetic performance the two newly identified genes were determined to be equal or better than ß-tubulin, ITS, and tef-1a in resolving relationships between species of Gnomoniopsis and Ophiognomonia. Differences in site specific rate of evolution in ß-tubulin, FG1093, ITS, MS204, and tef-1a were found. In addition, isolates from five classes, including 15 orders and 22 families, of Ascomycota were screened using the primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. Intron length variation for these 53 taxa in the Ascomycota was observed.