title: Polyploidy and the petal transcriptome of Gossypium raimondii
design: Plant Material   Six accessions were used in our study: G. arboreum (2x=2n=26, A2), G. raimondii (2x=2n=26, D5), G. tomentosum (4x=2n=52, AD3), G. hirsutum cv. Acala Maxxa (4x=2n=52, AD1; referred to as Maxxa), G. hirsutum cv. TX2094 (referred to as Tx) and a sterile diploid F1-hybrid between A2 and D5 (1x = 1n = 26; F1) (Table 1). The diploid F1-hybrid was created by a hand pollination between reduced gametes of diploids G. arboreum (A2) and G. raimondii (D5), and its somatic cells only contains 13 chromosomes from each extant diploid genome (Table 1).  Petal tissue was collected from plants growing under controlled greenhouse conditions at the Pohl Conservatory, Iowa State University, USA. Tissue was harvested at the time of full petal expansion after dawn but before pollination. Taking one flower from three different plants made three biological replicates for experiments. Harvested tissue was flash frozen in liquid nitrogen and stored at -80o C until RNA and DNA extraction.     RNA extractions, RNA-Seq Libraries and Sequencing  RNA samples were extracted from the three replicates using a modified hot borate method [31]. RNA samples were quantified using Ribogreen (Invitrogen Inc., Grand Island, NY) and their quality was evaluated on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). As described by Illumina, cDNA was sheared by sonication to a 200-400 bp fragment size (Covaris Inc., Woburn, MA).  RNA seq libraries were prepared according to the Illumina TruSeq RNA library prep kit protocol and sequenced on an Illumina HiSeq using v.2 chemistry at the Huntsman Cancer Center, SLC, UT.