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Research article2015Peer reviewed

The primer fITS9 prevents chimera formation during fungal DNA amplification in a bark beetle DNA background

Strid, Ylva; Ihrmark, Katarina; Stenlid, Jan


Insects are frequently associated with fungi in natural habitats. Molecular detection of fungal species using the primer pair ITS1F and ITS4 to amplify the ribosomal ITS region has become standard for studies of fungal ecology. When addressing insect and fungal DNA together, sequencing of the ITS region often results in chimeras due to ITS4 binding to both insect and fungal DNA. Using the newly developed primer fITS9, placed in the 5.8S region in the middle of the ITS region, we show that chimeras (insect-fungal, fungal-fungal, fungal-plants or fungal-mammals) can be avoided and a shorter and less variable DNA sequence product can be obtained. This method allows a more targeted amplification of fungal DNA from mixed samples and decreases the necessity for a nested PCR approach.

Published in

Forest Pathology
2015, Volume: 45, number: 1, pages: 9-13