Identification and the potential roles of long non-coding RNAs in cotton leaves damaged by Aphis gossypii

Long non-coding RNAs (lncRNAs) belong to a family of regulatory RNAs of non-coding RNAs (ncRNAs). They play essential roles in plant various developmental processes and stress responses. However, lncRNA functions in cotton are rarely known under attack of cotton aphids (Aphis gossypii Glover). Herein, we performed whole-transcriptome RNA sequencing for cotton four-leaf-stage leaves (Gossypium hirsutum, ZM-03199) damaged by cotton aphids at different time stages (6, 12, 24, 48, and 72 h) and without cotton aphid damage (0 h). We identified 8414 lncRNAs in 6 RNA-Seq data, including 6516 intergenic lncRNAs (77%), 759 anti-sense lncRNAs (7%), 334 intronic lncRNAs (4%) and 805 (10%) sense lncRNAs. Furthermore, 1331 lncRNAs showed differential expressions, and the gene ontology (Go) and KEGG analysis discovered that many target protein-coding genes of lncRNAs were enriched in stress-related categories. In addition, a total of 55 lncRNAs among 8414 lncRNAs were predicted as target mimics of cotton 285 miRNAs. Real-time quantitative PCR (qPCR) confirmed that all selected lncRNAs were relative to aphid damage. These results laid a solid foundation for the study of cotton lncRNA functions under the damage of cotton aphids.