caa a22 4500 445821442 CHVBK 20180317145245.0 cr unu---uuuuu 170323e20110201xx s 000 0 eng 10.1007/s00239-010-9414-3 doi (NATIONALLICENCE)springer-10.1007/s00239-010-9414-3 Poly(T) Variation in Heteroderid Nematode Mitochondrial Genomes is Predominantly an Artefact of Amplification [Elektronische Daten] [Angelique Riepsamen, Tracey Gibson, Janet Rowe, David Chitwood, Sergei Subbotin, Mark Dowton] We assessed the rate of in vitro polymerase errors at polythymidine [poly(T)] tracts in the mitochondrial DNA (mtDNA) of a heteroderid nematode (Heterodera cajani). The mtDNA of these nematodes contain unusually high numbers of poly(T) tracts, and have previously been suggested to contain biological poly(T) length variation. However, using a cloned molecule, we observed that poly(T) variation was generated in vitro at regions containing more than six consecutive Ts. This artefactual error rate was estimated at 7.3×10−5 indels/poly(T) tract>6 Ts/cycle. This rate was then compared to the rate of poly(T) variation detected after the amplification of a biological sample, in order to estimate the ‘biological+artefactual' rate of poly(T) variation. There was no significant difference between the artefactual and the artefactual+biological rates, suggesting that the majority of poly(T) variation in the biological sample was artefactual. We then examined the generation of poly(T) variation in a range of templates with tracts up to 16 Ts long, utilizing a range of Heteroderidae species. We observed that T deletions occurred five times more frequently than insertions, and a trend towards increasing error rates with increasing poly(T) tract length. These findings have significant implications for studies involving genomes with many homopolymer tracts. Springer Science+Business Media, LLC, 2010 Polythymidine nationallicence Mitochondrial DNA nationallicence Heteroderidae nationallicence Polymerase slippage nationallicence Amplification artefacts nationallicence Homopolymer nationallicence Nematode nationallicence Riepsamen Angelique School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut Gibson Tracey School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut Rowe Janet Nematode Interactions Unit, Rothamsted Research, AL5 2JQ, Harpenden, Hertfordshire, UK aut Chitwood David Nematology Laboratory, United States Department of Agriculture, Agricultural Research Service, 20705, Beltsville, MD, USA aut Subbotin Sergei Plant Pest Diagnostics Center, California Department of Food and Agriculture, 3294 Meadowview Road, 95832-1448, Sacramento, CA, USA aut Dowton Mark School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut Journal of Molecular Evolution Springer-Verlag 72/2(2011-02-01), 182-192 0022-2844 72:2<182 2011 72 239 https://doi.org/10.1007/s00239-010-9414-3 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-010-9414-3 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Riepsamen Angelique School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut NATIONALLICENCE 700 1- Gibson Tracey School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut NATIONALLICENCE 700 1- Rowe Janet Nematode Interactions Unit, Rothamsted Research, AL5 2JQ, Harpenden, Hertfordshire, UK aut NATIONALLICENCE 700 1- Chitwood David Nematology Laboratory, United States Department of Agriculture, Agricultural Research Service, 20705, Beltsville, MD, USA aut NATIONALLICENCE 700 1- Subbotin Sergei Plant Pest Diagnostics Center, California Department of Food and Agriculture, 3294 Meadowview Road, 95832-1448, Sacramento, CA, USA aut NATIONALLICENCE 700 1- Dowton Mark School of Biological Sciences, University of Wollongong, 2522, Wollongong, NSW, Australia aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 72/2(2011-02-01), 182-192 0022-2844 72:2<182 2011 72 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer