Genome-wide identification, characterization and expression analysis of long non-coding RNAs in different tissues of apple

Recently, the long non-coding RNAs (lncRNAs), which play important roles in various complex biological processes, have received more attention in plants. However, little information is available on lncRNAs in woody fruit trees and their potential regulatory roles remain poorly understood, especially in apple. Here, a total of 1726 high-confidence lncRNAs (hc-IncRNAs) were identified in different tissues including young fruits, shoot tips, stem phloem and root tips using high-throughput sequencing. These lncRNAs are distributed across all 17 apple chromosomes, and > 85% come from intergenic regions. The apple lncRNAs have longer transcript lengths and greater exon numbers than protein-coding genes. Additionally, among the 1726 hc-IncRNA, 850 are predicted to have target genes. These target genes are involved in many processes including hormone signaling, sugar metabolism, and the cell cycle and stress responses. Furthermore, 57, 74, 168 and 78 lncRNAs specifically expressed in root tips, shoot tips, young fruits and stem phloem were analyzed using the COG (cluster of orthologous group)and GO (gene ontology) databases. Young fruits contain the most unique lncRNAs, which are involved in biological processes such as energy production and conversion, carbohydrate transport and metabolism, posttranslational modification and protein turnover. Quantitative real-time PCR (qRT-PCR) is employed to confirm the different expression levels among the four tissues. Moreover, the expression levels of eight fruit related lncRNAs are investigated during different fruit development stages, which indicates they have important roles in fruit ripening and sugar metabolism. Overall, our genome-wide research on lncRNAs in different apple tissues provides valuable clues and information that can help elucidate the potential roles of lncRNAs in the growth and development of apple, as well as in other fruit trees.