title: Identification and evolutionary analysis of long non-coding RNAs in zebra finch.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.|Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Chih-Kuan
authors.initials: CK
authors.lastname: Chen
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Chun-Ping
authors.initials: CP
authors.lastname: Yu
authors.affiliation: Department of Medical Research, Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan.
authors.forename: Sung-Chou
authors.initials: SC
authors.lastname: Li
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Siao-Man
authors.initials: SM
authors.lastname: Wu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Mei-Yeh Jade
authors.initials: MJ
authors.lastname: Lu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Yi-Hua
authors.initials: YH
authors.lastname: Chen
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
authors.forename: Di-Rong
authors.initials: DR
authors.lastname: Chen
authors.affiliation: Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan. gcsng@life.nthu.edu.tw.
authors.forename: Chen Siang
authors.initials: CS
authors.lastname: Ng
authors.affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan. ctting@ntu.edu.tw.|Department of Life Science & Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 10617, Taiwan. ctting@ntu.edu.tw.|Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan. ctting@ntu.edu.tw.
authors.forename: Chau-Ti
authors.initials: CT
authors.lastname: Ting
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. whli@sinica.edu.tw.|Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. whli@sinica.edu.tw.|Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA. whli@sinica.edu.tw.
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D046369:Finches / Q000235:genetics*; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding
keywords: Feather development; Zebra finch; lncRNA; ssRNA-seq