RNA-Seq of CK_3
Total RNAs were extracted from CK_3 stigmas using RNAprep Pure Plant Plus Kit (Tiangen, Beijing, China). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity and concentration were measured by NanoDrop 2000 (Thermo Scientific, DE, USA). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). The qualified RNA samples were used for cDNA libraries construction by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturers instructions. The libraries were evaluated on the Agilent Bioanalyzer 2100 system and sequenced on Illumina HiSeq 2000 platform.Raw data was preprocessed to generate clean data by removing reads containing adapter, reads containing ploy-N and low quality reads. The paired-end clean reads were aligned to the sweetpotato genome (http://public-genomes-ngs.molgen.mpg.de/SweetPotato/) using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. The gene expression level was estimated by FPKM (Fragments per kilo base of transcript per million mapped reads) calculation based on the length of the gene and reads count mapped to this gene. Differential expression analysis of FT vs CK, MFT vs CK, MFT vs MT and MFT vs FT were performed using the DESeq R package (1.18.0). Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.