Oregon Undergraduate Research Journal: Vol. 9 No. 1 (2015)

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Xylaria Primers for Phylogenetic Reconstruction
(University of Oregon, 2015) Ly, Alicia
Xylaria is a genus of Ascomycete fungi that is comprised of an estimated 400 species. These species are important to the ecosystems in which they inhabit because they contribute to the decomposition of wood, which recycles lignin and cellulose. Though the morphological traits of this genus have been widely studied over the years, their molecular phylogenetics have not been extensively explored due to the historical unavailability of species genomes. Now that complete genomes have become available, there have been an increasing number of ribosomal Internal Transcribed Spacer (ITS) sequence studies in recent years. However, ITS is too variable to consistently construct accurate phylogenetic trees, so Xylaria phylogeny is still being researched. This study explores the use of single-copy genes as an alternative to ITS methods. Here we present three primer pairs for different single-copy genes for use during future phylogenetic evaluation of Xylaria. These primers, Splicing Factor PRP43 F1054/R1691, MCM5 F409/R1059 and 40S Ripro S3Ae F47/R605, are more reliable than ITS sequences for deeper levels of analysis due to less variability in their sequences. This study focuses on Xylaria, while utilizing related species within in the Xylariaceae and Sordariaceae families, providing a promising start to the complete reconstruction of the Xylaria phylogenetic tree.