Location: Fruit and Tree Nut ResearchTitle: Metagenomics characterization of wood decay fungi colonized in peach limb heartwood
|Hotchkiss, Michael - Mike|
|GARBELOTTO, MATTEO - UNIVERSITY OF CALIFORNIA|
Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/12/2015
Publication Date: 1/9/2016
Citation: Chen, C., Bock, C.H., Hotchkiss, M.W., Garbelotto, M.M., Cottrell, T.E. 2016. Metagenomics characterization of wood decay fungi colonized in peach limb heartwood. Plant and Animal Genome Conference. 22:224.
Interpretive Summary: Expressed sequence tag (EST) simple sequence repeat (SSR) markers have been widely used in trait linkage analysis, gene mapping, variety authentication and other genetic studies. However, it is wasteful because some randomly selected EST-SSR primers fail to detect and/or lack polymorphism. A look into genomic factors in EST-SSR primers and amplicons potentially associated with these failures and/or polymorphisms can provide helpful guidance on selection of primers with better successful rate and polymorphism.
Technical Abstract: Breakage of healthy-looking scaffold limbs is commonly seen in peach orchards in central Georgia, in the United States, and may have impact on the health and longevity of peach trees. White fungal mycelia were observed on the broken surface of some newly snapped, but otherwise healthy-looking peach scaffold limbs. Cross-cut limb sections from apparently healthy scion cultivars were collected and incubated under high humidity for 2 weeks. Fungal growth was observed on the cross-cut surface in two repeated experiments. In this study, genomic DNAs were extracted from the fungus growing on surface of the cross-cut sections. Using next-generation sequencing technology and metagenomic analysis, two white-rot fungi, Trametes versicolor and Schizophyllum commune, were deemed to be the most likely fungi colonizing the heartwood in these specimens. The former likely was predominant over the latter partly because there was a much greater number of read alignments onto the sequences from the T. versicolor genome than that from the S. commune genome. The co-existence of the two fungi were confirmed by Sanger sequencing of an internal transcribed spacer (ITS) amplicon and amplicons from new primers designed from selected contigs, as two different fragments of similar sizes were amplified by the ITS and most selected primers from the DNA extracted from the specimens. Possible reasons for the white-rot fungi colonizing and growing within the peach limbs of apparently healthy, living trees are discussed, as are the likely impact of the colonization on the peach tree health. Further research needs are considered.