Citrus unshiu Transcriptome or Gene expression
To future examine more globally genes that may be responsive to CsFUS3 accumulation, we used RNA-seq to compare the transcriptome profiles of the overexpression line with that of empty vector line at two representative time points during SE. After removing low-quality reads, about 13 million reads per sample were mapped against sweet orange reference genome. Using FDR=0.001 and Abs [log(fold-change)] =1 as a selection threshold, a total of 329 genes were found differentially expressed in the CsFUS3 OE line after 6 weeks of induction, including 227 up-regulated and 102 down-regulated genes. Of the 1,895 DEGs at 12 weeks, 1,165 were up-regulated and 730 down-regulated in OE line, indicating a large transcriptional reprogramming in the transgenic callus at later stages of SE RNA-Seq transcriptome profiling revealed that a number SE-promotive TF genes were up-regulated in the overexpression line. In addition, the expression of pathway genes involved in biosynthesis, deactivation, and signaling of ABA and GA was altered. Overall design: Compare the transcriptome profiles of the overexpression line with that of empty vector line at two representative time points during SE: the onset of the somatic embryo emergence (12 weeks after induction), and the earlier time point when the colour just began to change (6 weeks after induction). Libraries were sequenced by lon Proton platform, two biological replicates for each sample. Please note that the previous study (PMID 24489955) has done annotation project of Citrus sinensis.The database web link is http://citrus.hzau.edu.cn/. However, this web link is not functional yet. Thus the annotation .gff3 file is provided in the meantime.