caa a22 4500 475793854 CHVBK 20180406123718.0 cr unu---uuuuu 170329e20000801xx s 000 0 eng 10.1007/s001220051498 doi (NATIONALLICENCE)springer-10.1007/s001220051498 S1 analysis of long PCR heteroduplexes: detection of chloroplast indel polymorphisms in Fragaria [Elektronische Daten] [J. Lin, T. M. Davis] Abstract : S1 analysis of long PCR heteroduplexes was found to be an effective method for detecting phylogenetically informative indel (insertion/deletion) polymorphisms in the highly conserved strawberry chloroplast genome. In this broadly applicable method, long-range PCR products containing heteroduplex DNA molecules generated from mixed-template amplifications are subjected to S1 nuclease digestion followed by separation and visualization on an agarose gel. The presence of fragments resulting from S1 digestion of mismatch loops in heteroduplex molecules is indicative of indel polymorphism between the template sources. Upon analysis of 13-kb heteroduplex-containing PCR products spanning the petA-psbB chloroplast genome region in Fragaria vesca and Fragaria moschata, two indels distinguishing these species were detected, and subsequently localized to the psbJ-psbL and rpl20-rps18 intergenic regions. Comparative sequencing of these regions revealed that F. moschata resembled Fragaria viridis, but differed from F. vesca, Fragaria nubicola, and a closely related outgroup representative, Duchesnea indica, by a 10-bp deletion in the psbJ-psbL region and a 10-bp insertion in the rpl20-rps18 region. Thus, of the three diploids (2n = 2x = 14) examined, F. viridis is favored over F. vesca and F. nubicola as the most likely chloroplast genome donor to hexaploid (2n = 6x = 42) F. moschata. Springer-Verlag Berlin Heidelberg, 2000 Key words Fragaria nationallicence Heteroduplex nationallicence Indel nationallicence Phylogenetics nationallicence Strawberry nationallicence S1 nuclease nationallicence Lin J. Plant Biology Department, Rudman Hall, University of New Hampshire, Durham, NH 03824 USA e-mail: tom.davis@unh.edu, US aut Davis T. M. Plant Biology Department, Rudman Hall, University of New Hampshire, Durham, NH 03824 USA e-mail: tom.davis@unh.edu, US aut https://doi.org/10.1007/s001220051498 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s001220051498 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Lin J. Plant Biology Department, Rudman Hall, University of New Hampshire, Durham, NH 03824 USA e-mail: tom.davis@unh.edu, US aut NATIONALLICENCE 700 1- Davis T. M. Plant Biology Department, Rudman Hall, University of New Hampshire, Durham, NH 03824 USA e-mail: tom.davis@unh.edu, US aut Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer