Using extensive sampling of root tissue across seasonal development and next-generation sequencing we have generated a reliable North American ginseng transcriptome with extensive annotation and isoform information.
All samples were composed of root tissue from four individual plants, all grown in the same hydroponic unit.
Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots).
following wounding of root tissue (see Fig. 3H).
For pixel detection of root tissue, individual plants could be assessed, since root tissue did not overlap between separate clones.
Transcriptome sequencing of three independent biological samples of four root tissues yielded a total of 262,151,698 raw RNA-seq reads from pair of 131,075,849 reads (Table 1).
Samples of transgenic root tissues were collected in liquid nitrogen and preserved (−80°C) until tested.
Specific collection information, including sampling location, tissue type, sampling time, and application are shown in Additional file 7. Root samples used in the M. × giganteus sequencing project were collected from rhizomes grown in the greenhouse in calcinated clay (Turface) in order to increase the efficiency of root-tissue sampling.
Among all samples, root tissue had the lowest number of transcripts of all PfDGATs.
Dry samples of root and shoot tissue were ground and ashed at 495 °C for 12 h.
50 mg samples of root and shoot tissue were harvested at different time points after treatment, homogenized and suspended in CCLR buffer (Promega Corp. Madison, USA).
