Fall2013 S. lycopersicum chloroplast resequencing
A 2-3 gm sample of fresh-frozen leaf tissue was used, harvested from 15         cultivars. After chloroform extraction, RNaseA and Proteinase K digestion, incubation in         high salt, and a second phenol-chloroform extraction the material was precipitated with         isopropanol and quantified using a Nanodrop 2000. The chloroplast genome was then amplified         using overlapping primers that give ~15,000 bp amplicons. Primers and conditions available         upon request, and will be published. We ligated bar-coded adaptors using the Ion Xpress kit.         The library was quantified using the Kapa Biosystems kit for the Ion Torrent and BioRad         iCycler. After appropriate dilutions, emPCR was performed using the Ion 400bp kit reagents         and conditions for the Ion OneTouch2 instrument. Confirmation of ISP loading with the Qubit         was followed by sequencing of the libraries on the Ion Torrent PGM, using the 400bp         sequencing kit. Data was generated at the University of North Carolina at Charlotte in Fall         Term 2013 by Koyt Everhart, Terrence Gelineau, Lindsay Heater, Anuja Jain, Myung Sik Jeon,         Frederick Lin, Ibro Mujacic, Lara Murphy, Jamie Shuman, Sushant Patil, Cathy Moore, and         Lawrence Marcus under the supervision of Dr. Jennifer Weller and Jonathan Shea. Data was         prepared for submission by Robert Player, Christopher Ball, Brandon Burciaga, Harini         Saravanan, Joshua Cepeda, Thany Seyok, Daniel Zyska, and Ana Camposeco-Jacobs under the         supervision of Dr. Cynthia Gibas.