Endophytic fungal DNA, the source of contamination in spruce needle DNA

Abstract

DNA isolated and amplified from higher plants may originate from symbiotic microbes occupying plant tissues. A recent report on the phylogeny of Picea contained sequence data that upon later analysis proved to originate from filamentous ascomycetes. Isolates of endophytic fungi from Picea foliage collected from the same location as the original samples were examined to identify the source of the contaminating DNA. The ITS region of isolates was screened by Southern blotting using an oligonucleotide probe homologous to a unique portion of the reported ‘spruce’ sequences. This study identifies a DNA sequence originally attributed to Picea engelmannii (Engelmann spruce) as Hormonema dematioides, a ubiquitous foliar endophyte of conifers. Infections of plants by endophytic fungi are common and their presence is not revealed by external symptoms. Plant molecular researchers should be aware of the potential for this type of DNA contamination.

Relationships among the Spruces (Picea, Pinaceae) of Southwestern North America

“…Picea pungens and P. engelmannii were also reported to be members of different clades based on nuclear ribosomal 18s sequences and an internal transcribed spacer (Smith and Klein 1994), but this work was shown to be in error (Smith and Klein 1996;Camacho et al 1997). The ribosomal 18s sequences were actually from an endophytic fungus, Hormonema dematioides (Camacho et al 1997). Picea pungens did cluster with P. engelmannii in an investigation based on random ampli ed polymorphic DNA (Nkongolo 1999), but neither P. chihuahuana nor P. martinezii were included in that study.…”

“…However, P. pungens also joined a P. chihuahuana clade in Sigurgeirsson's (1992) UPGMA tree that was based on cpDNA restriction fragment polymorphisms. Picea pungens and P. engelmannii were also reported to be members of different clades based on nuclear ribosomal 18s sequences and an internal transcribed spacer (Smith and Klein 1994), but this work was shown to be in error (Smith and Klein 1996;Camacho et al 1997). The ribosomal 18s sequences were actually from an endophytic fungus, Hormonema dematioides (Camacho et al 1997).…”

Ecological Implications of Anti-Pathogen Effects of Tropical Fungal Endophytes and Mycorrhizae

“…Therefore, it should not be surprising then that E+ plant tissues have been found to exhibit different chemical profiles from E-plant tissues (Petrini et al 1992, Saikkonen et al 1998, Yue et al 2000, 2001; L. C. Mejia, T. Gianfagna, and E. A. Herre, unpublished manuscript). Even genetic content that has been attributed to being of plant origin sometimes turns out to be derived from the fungi (Camacho et al 1997, Chiang et al 2001, Saar et al 2001.…”

Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus

“…They have been inadvertently isolated and PCR-amplified from plant tissues in several phylogenetic projects using ITS sequences (Liston and Alvarez-Buylla, 1995;Hershkovitz and Lewis, 1996;Hershkovitz and Zimmer, 1996;Liston et al, 1996;Camacho et al, 1997;Coleman and Mai, 1997;Zhang et al, 1997). Fungal and chlorophycean ITS sequences have supplanted those of Picea (Bobola et al, 1992;Smith and Klein, 1994) and Mimulus .…”