Identification and evolutionary analysis of long non-coding RNAs in zebra finch

• DOI: 10.1186/s12864-017-3506-z
• Publication Date: 2017-01-31T04:20:17Z
• Authors: Chih-Kuan Chen; Chun-Ping Yu; Sung-Chou Li; Siao-Man Wu; Mei-Yeh Jade Lu; Yi-Hua Chen; Di-Rong Chen; Chen Siang Ng; Chau-Ti Ting; Wen-Hsiung Li
• Keywords: Conserved sequence; RNA-Seq

Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, further evolutionary conservation of birds amniotes. A total 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic 57 antisense (lncNATs), were identified using our newly developed pipeline. These avian share similar characteristics with mammals, such as shorter transcript length, lower exon number, average expression level less sequence than mRNAs. However, proportion overlapping transposable elements is much that mammals. We predicted functions based enriched co-expressed protein-coding genes. Clusters associated natal down development identified. The sequences levels candidate shared conserved among validated by qPCR both chicken. Finally, three highly may be Our study provides first systematical identification ssRNA-seq analysis offers a resource embryonically finch. also function lncRNAs.