1. Identification and evolutionary analysis of long non-coding RNAs in zebra finch
- Author
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Chih-Kuan Chen, Chun-Ping Yu, Chen Siang Ng, Siao-Man Wu, Wen-Hsiung Li, Sung-Chou Li, Yi-Hua Chen, Di-Rong Chen, Chau-Ti Ting, and Mei-Yeh Jade Lu
- Subjects
0301 basic medicine ,animal structures ,Biology ,Proteomics ,Conserved sequence ,Transcriptome ,Evolution, Molecular ,03 medical and health sciences ,Exon ,lncRNA ,ssRNA-seq ,Genetics ,Animals ,Cluster Analysis ,Zebra finch ,Gene ,Gene Expression Profiling ,Computational Biology ,Genomics ,biology.organism_classification ,Feather development ,030104 developmental biology ,Evolutionary biology ,RNA, Long Noncoding ,Finches ,DNA microarray ,Taeniopygia ,Biotechnology ,Research Article - Abstract
Background Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes. Results A total of 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic lncRNAs, and 57 antisense lncRNAs (lncNATs), were identified using our newly developed pipeline. These avian IncRNAs share similar characteristics with lncRNAs in mammals, such as shorter transcript length, lower exon number, lower average expression level and less sequence conservation than mRNAs. However, the proportion of lncRNAs overlapping with transposable elements in birds is much lower than that in mammals. We predicted the functions of IncRNAs based on the enriched functions of co-expressed protein-coding genes. Clusters of lncRNAs associated with natal down development were identified. The sequences and expression levels of candidate lncRNAs that shared conserved sequences among birds were validated by qPCR in both zebra finch and chicken. Finally, we identified three highly conserved lncRNAs that may be associated with natal down development. Conclusions Our study provides the first systematical identification of avian lncRNAs using ssRNA-seq analysis and offers a resource of embryonically expressed lncRNAs in zebra finch. We also predicted the biological function of identified lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3506-z) contains supplementary material, which is available to authorized users.
- Published
- 2017