Design: 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.
Submitted by: University of North Carolina at Charlotte
Study:
Solanum lycopersicum strain:Cherry, Purple Calabash, LA2377, Yellow Tomato, Hardin's Miniature Tomato, Baxter's Early Bush Cherry, German Cherry, Heinz 1706-BG, Black Cherry, Cherokee Purple, Delicious, Jersey Devil, Yellow Stuffer, Mortgage Lifter Targeted Locus (Loci)show Abstracthide AbstractResequencing of tomato cultivar chloroplasts
Sample:
Chloroplast genome sequencing data using IonTorrent PGMLibrary:
Name: pooled 2013
Instrument: Ion Torrent PGM
Strategy: AMPLICON
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
1 forward
Runs:
1 run, 334,923 spots, 50.1M bases, 38.7Mb