ABSTRACT: Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.
