Prediction, analysis and identification of long, non-coding RNA in the midguts of Apis mellifera ligustica workers

Author of the article:XIONG Cui-Ling** GENG Si-Hai** WANG Xin-Rui LIU Si-Ya CHEN Da-Fu ZHENG Yan-Zhen FU Zhong-Min

Author's Workplace：College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Chin

Key Words：Apis mellifera ligustica, midgut, lncRNA-seq technology, long non-coding RNA, upstream and downstream genes

Abstract： [Objectives]  To predict, analyze and identify lncRNAs in the midguts of Apis mellifera ligustica workers, and investigate their functions. [Methods]  The midguts of A. m. ligustica workers were sequenced with a combination of lncRNA-seq technology and strand-specific cDNA library construction method; the raw data was filtered with perl script; lncRNAs were predicted using CPC and CNCI softwares, and their characteristics were compared with those of adjacent protein-coding genes; RT-PCR was used to identify randomly selected lncRNAs; GO classification and KEGG pathway enrichment analyses of lncRNAs’ upstream and downstream genes were carried out using the related bioinformatic software. [Results]  A total of 1 956 118 858 raw reads were obtained from the deep sequencing of midgut samples, and 1 946 489 304 clean reads were obtained after filtering. In total, 6 353 lncRNAs were predicted. Compared with protein-coding genes, these lncRNAs genes had fewer exons and shorter transcripts. The expression of nine lncRNAs was identified. Further investigation showed that up- and down-stream genes of A. m. ligustica lncRNAs were enriched in 42 GO terms and 256 pathways. Moreover, these lncRNAs are found to be engaged in the metabolism and cell-life activity in the midgut of A. m. ligustica worker. [Conclusion]   These results not only enrich the information of honeybee lncRNAs, but also provide a foundation for revealing the role of lncRNAs during the development and stress response processes in the A. m. ligustica worker midgut.