title: Transcriptomic analyses of regenerating adult feathers in chicken.
abstract: BACKGROUND
  Feathers have diverse forms with hierarchical branching patterns and are an excellent model for studying the development and evolution of morphological traits. The complex structure of feathers allows for various types of morphological changes to occur. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet there is only limited relevant information for gene expression during feather development.
  
  
  RESULTS
  We conducted transcriptomic analysis of five zones of feather morphologies from two feather types at different times during their regeneration after plucking. The expression profiles of genes associated with the development of feather structure were examined. We compared the gene expression patterns in different types of feathers and different portions of a feather and identified morphotype-specific gene expression patterns. Many candidate genes were identified for growth control, morphogenesis, or the differentiation of specific structures of different feather types.
  
  
  CONCLUSIONS
  This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis. It significantly increased our understanding of the complex molecular and cellular events in feather development processes and provided a foundation for future studies on the development of other skin appendages.
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. gcsng@gate.sinica.edu.tw.
authors.forename: Chen Siang
authors.initials: CS
authors.lastname: Ng
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. r93b42016@gmail.com.|Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan. r93b42016@gmail.com.
authors.forename: Chih-Kuan
authors.initials: CK
authors.lastname: Chen
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. alangfan@gmail.com.|Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, 20401, Taiwan. alangfan@gmail.com.
authors.forename: Wen-Lang
authors.initials: WL
authors.lastname: Fan
authors.affiliation: Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. Ping.Wu@med.usc.edu.
authors.forename: Ping
authors.initials: P
authors.lastname: Wu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. u941671@oz.nthu.edu.tw.
authors.forename: Siao-Man
authors.initials: SM
authors.lastname: Wu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. Madvulcan0824@msn.com.
authors.forename: Jiun-Jie
authors.initials: JJ
authors.lastname: Chen
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. oswald1207@gmail.com.
authors.forename: Yu-Ting
authors.initials: YT
authors.lastname: Lai
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. jimmau@gate.sinica.edu.tw.
authors.forename: Chi-Tang
authors.initials: CT
authors.lastname: Mao
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. meiyehlu@gate.sinica.edu.tw.
authors.forename: Mei-Yeh Jade
authors.initials: MY
authors.lastname: Lu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. cherrychen2835@gmail.com.
authors.forename: Di-Rong
authors.initials: DR
authors.lastname: Chen
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. terrylin17@gmail.com.
authors.forename: Ze-Shiang
authors.initials: ZS
authors.lastname: Lin
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. kwish101@gmail.com.
authors.forename: Kai-Jung
authors.initials: KJ
authors.lastname: Yang
authors.affiliation: Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan. shasha0919@yahoo.com.tw.
authors.forename: Yuan-An
authors.initials: YA
authors.lastname: Sha
authors.affiliation: Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan. tctu0523@gmail.com.
authors.forename: Tsung-Che
authors.initials: TC
authors.lastname: Tu
authors.affiliation: Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan. cfchen@dragon.nchu.edu.tw.|Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. cfchen@dragon.nchu.edu.tw.
authors.forename: Chih-Feng
authors.initials: CF
authors.lastname: Chen
authors.affiliation: Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. cmchuong@med.usc.edu.|Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. cmchuong@med.usc.edu.|Integrative Stem Cell Center, China Medical University, Taichung, 40402, Taiwan. cmchuong@med.usc.edu.
authors.forename: Cheng-Ming
authors.initials: CM
authors.lastname: Chuong
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.|Integrative Stem Cell Center, China Medical University, Taichung, 40402, 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; D002454:Cell Differentiation; D002645:Chickens / Q000235:genetics* / Q000254:growth & development; D005241:Feathers / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D009024:Morphogenesis / Q000235:genetics; D012038:Regeneration / Q000235:genetics*; D012867:Skin / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*