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Chen CK, Chang YM, Jiang TX, Yue Z, Liu TY, Lu J, Yu Z, Lin JJ, Vu TD, Huang TY, Harn HIC, Ng CS, Wu P, Chuong CM, Li WH. Conserved regulatory switches for the transition from natal down to juvenile feather in birds. Nat Commun 2024; 15:4174. [PMID: 38755126 PMCID: PMC11099144 DOI: 10.1038/s41467-024-48303-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We report that extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial-mesenchymal interactions for branching morphogenesis. α-SMA (ACTA2) compartmentalizes dermal papilla stem cells for feather renewal cycling. LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We show that this primary feather transition is largely conserved in chicken (precocial) and zebra finch (altricial) and discuss the possibility that this evolutionary adaptation process started in feathered dinosaurs.
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Affiliation(s)
- Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - ZhiCao Yue
- Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, Guangdong, China
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Tzu-Yu Liu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jiayi Lu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhou Yu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jinn-Jy Lin
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Trieu-Duc Vu
- Michigan Neuroscience Institute, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Tao-Yu Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chen Siang Ng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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Urban CA, Legendre LJ, Clarke JA. Description of natal down of the ostrich (Struthio camelus) and comparison with common quail (Coturnix coturnix): Developmental and evolutionary implications. J Anat 2023; 243:1007-1023. [PMID: 37515428 PMCID: PMC10641043 DOI: 10.1111/joa.13936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/18/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Natal down is a feather stage that differs in both form and function from the definitive feathers of adult birds. It has a simpler structure that has been speculated to be similar to the body coverings of non-avian dinosaurs. However, inference of the evolution of natal down has been limited by our understanding of its structural variation in extant birds. Most descriptive work has focused on neognathous birds, limiting our knowledge of the full diversity of feathers in extant taxa. Here, we describe the natal down of a post-hatch ostrich (Struthio camelus) and compare it to that of a post-hatch quail (Coturnix coturnix). We confirm the presence of featherless spaces (apteria) in S. camelus and the lack of barbules on the tips of natal down in both species. We also find differences between dorsal and ventral natal down structures, such as barbule density in S. camelus and the extent of the bare portion of the barb in both species. Surprisingly, we do not find that the neoptiles of either species follow the ideal morphologies for increasing insulation. Finally, we hypothesize that the different barb types present in S. camelus natal down result from a large addition of new barb ridges during development, which is not known except in feathers with a rachis. These results have implications for our understanding of how structure informs function and development in understudied feather types, such as those shared by non-avian dinosaurs.
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Affiliation(s)
- Carmen A Urban
- Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Lucas J Legendre
- Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Julia A Clarke
- Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proc Natl Acad Sci U S A 2022; 119:e2119602119. [PMID: 35733255 PMCID: PMC9245644 DOI: 10.1073/pnas.2119602119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Seadragons are widely recognized for their derived traits, which include leaf-like appendages and extreme spinal curvature. Efforts to understand the genetic basis of these unique traits and conserve these species and their relatives have been limited by genomic resource gaps. In this paper we present full, annotated genomes of leafy and weedy seadragons, which we use to uncover surprising features of gene family and genome architecture evolution that likely relate to the extravagant phenotypic traits of seadragons and their pipefish and seahorse relatives. These genomes and their analyses are important advances for the study of elaborate vertebrate traits, leveraging this diverse, morphologically exceptional group of fishes. Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.
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Wu Q, Liu H, Yang Q, Wei B, Wang L, Tang Q, Wang J, Xi Y, Han C, Wang J, Li L. Developmental Transcriptome Profiling of the Tibial Reveals the Underlying Molecular Basis for Why Newly Hatched Quails Can Walk While Newly Hatched Pigeons Cannot. Front Cell Dev Biol 2022; 10:745129. [PMID: 35198553 PMCID: PMC8858812 DOI: 10.3389/fcell.2022.745129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Birds can be classified into altricial and precocial species. The hatchlings of altricial birds cannot stand, whereas precocial birds can walk and run soon after hatching. It might be owing to the development of the hindlimb bones in the embryo stage, but the molecular regulatory basis underlying the divergence is unclear. To address this issue, we chose the altricial pigeon and the precocial Japanese quail as model animals. The data of tibia weight rate, embryonic skeletal staining, and tibia tissues paraffin section during the embryonic stage showed that the Japanese quail and pigeon have similar skeletal development patterns, but the former had a faster calcification rate. We utilized the comparative transcriptome approach to screen the genes and pathways related to this heterochronism. We separately analyzed the gene expression of tibia tissues of quail and pigeon at two consecutive time points from an inability to stand to be able to stand. There were 2910 differentially expressed genes (DEGs) of quail, and 1635 DEGs of pigeon, respectively. A total of 409 DEGs in common in the quail and pigeon. On the other hand, we compared the gene expression profiles of pigeons and quails at four time points, and screened out eight pairs of expression profiles with similar expression trends but delayed expression in pigeons. By screening the common genes in each pair of expression profiles, we obtained a gene set consisting of 152 genes. A total of 79 genes were shared by the 409 DEGs and the 152 genes. Gene Ontology analysis of these common genes showed that 21 genes including the COL gene family (COL11A1, COL9A3, COL9A1), IHH, MSX2, SFRP1, ATP6V1B1, SRGN, CTHRC1, NOG, and GDF5 involved in the process of endochondral ossification. These genes were the candidate genes for the difference of tibial development between pigeon and quail. This is the first known study on the embryo skeletal staining in pigeon. It provides some new insights for studying skeletal development mechanisms and locomotor ability of altricial and precocial bird species.
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Folding Keratin Gene Clusters during Skin Regional Specification. Dev Cell 2021; 53:561-576.e9. [PMID: 32516596 DOI: 10.1016/j.devcel.2020.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023]
Abstract
Regional specification is critical for skin development, regeneration, and evolution. The contribution of epigenetics in this process remains unknown. Here, using avian epidermis, we find two major strategies regulate β-keratin gene clusters. (1) Over the body, macro-regional specificities (scales, feathers, claws, etc.) established by typical enhancers control five subclusters located within the epidermal differentiation complex on chromosome 25; (2) within a feather, micro-regional specificities are orchestrated by temporospatial chromatin looping of the feather β-keratin gene cluster on chromosome 27. Analyses suggest a three-factor model for regional specification: competence factors (e.g., AP1) make chromatin accessible, regional specifiers (e.g., Zic1) target specific genome regions, and chromatin regulators (e.g., CTCF and SATBs) establish looping configurations. Gene perturbations disrupt morphogenesis and histo-differentiation. This chicken skin paradigm advances our understanding of how regulation of big gene clusters can set up a two-dimensional body surface map.
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Ji G, Zhang M, Liu Y, Shan Y, Tu Y, Ju X, Zou J, Shu J, Wu J, Xie J. A gene co‐expression network analysis of the candidate genes and molecular pathways associated with feather follicle traits of chicken skin. J Anim Breed Genet 2020; 138:122-134. [DOI: 10.1111/jbg.12481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/23/2020] [Accepted: 04/03/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Gai‐ge Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yi‐fan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yan‐ju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yun‐jie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Xiao‐jun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jian‐min Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jing‐ting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jun‐feng Wu
- Jiangsu Li‐hua Animal Husbandry Company Jiangsu China
| | - Jin‐fang Xie
- Jiangxi Academy of Agricultural Sciences Nanchang China
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Hu X, Zhang X, Liu Z, Li S, Zheng X, Nie Y, Tao Y, Zhou X, Wu W, Yang G, Zhao Q, Zhang Y, Xu Q, Mou C. Exploration of key regulators driving primary feather follicle induction in goose skin. Gene 2020; 731:144338. [PMID: 31923576 DOI: 10.1016/j.gene.2020.144338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
The primary feather follicles are universal skin appendages widely distributed in the skin of feathered birds. The morphogenesis and development of the primary feather follicles in goose skin remain largely unknown. Here, the induction of primary feather follicles in goose embryonic skin (pre-induction vs induction) was investigated by de novo transcriptome analyses to reveal 409 differentially expressed genes (DEGs). The DEGs were characterized to potentially regulate the de novo formation of feather follicle primordia consisting of placode (4 genes) and dermal condensate (12 genes), and the thickening of epidermis (5 genes) and dermal fibroblasts (17 genes), respectively. Further analyses enriched DEGs into GO terms represented as cell adhesion and KEGG pathways including Wnt and Hedgehog signaling pathways that are highly correlated with cell communication and molecular regulation. Six selected Wnt pathway genes were detected by qPCR with up-regulation in goose skin during the induction of primary feather follicles. The localization of WNT16, SFRP1 and FRZB by in situ hybridization showed weak expression in the primary feather primordia, whereas FZD1, LEF1 and DKK1 were expressed initially in the inter-follicular skin and feather follicle primordia, then mainly restricted in the feather primordia. The spatial-temporal expression patterns indicate that Wnt pathway genes DKK1, FZD1 and LEF1 are the important regulators functioned in the induction of primary feather follicle in goose skin. The dynamic molecular changes and specific gene expression patterns revealed in this report provide the general knowledge of primary feather follicle and skin development in waterfowl, and contribute to further understand the diversity of hair and feather development beyond the mouse and chicken models.
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Affiliation(s)
- Xuewen Hu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xiaokang Zhang
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Zhiwei Liu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Shaomei Li
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xinting Zheng
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yangfan Nie
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yingfeng Tao
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xiaoliu Zhou
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Wenqing Wu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Ge Yang
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Qianqian Zhao
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Chunyan Mou
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China.
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9
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Feather Evolution from Precocial to Altricial Birds. Zool Stud 2019; 58:e24. [PMID: 31966325 DOI: 10.6620/zs.2019.58-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022]
Abstract
Birds are the most abundant terrestrial vertebrates and their diversity is greatly shaped by the feathers. How avian evolution is linked to feather evolution has long been a fascinating question. Numerous excellent studies have shed light on this complex relationship by investigating feather diversity and its underlying molecular mechanisms. However, most have focused on adult domestic birds, and the contribution of feather diversity to environmental adaptation has not been well-studied. In this review, we described bird diversity using the traditional concept of the altricial-precocial spectrum in bird hatchlings. We combined the spectrum with a recently published avian phylogeny to profile the spectrum evolution. We then focused on the discrete diagnostic character of the spectrum, the natal down, and propose a hypothesis for the precocial-to-altricial evolution. For the underlying molecular mechanisms in feather diversity and bird evolution, we reviewed the literature and constructed the known mechanisms for feather tract definition and natal down development. Finally, we suggested some future directions for research on altricial-precocial divergence, which may expand our understanding of the relationship between natal down diversity and bird evolution.
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Ng CS, Li WH. Genetic and Molecular Basis of Feather Diversity in Birds. Genome Biol Evol 2018; 10:2572-2586. [PMID: 30169786 PMCID: PMC6171735 DOI: 10.1093/gbe/evy180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago
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Chen CK, Yu CP, Li SC, Wu SM, Lu MYJ, Chen YH, Chen DR, Ng CS, Ting CT, Li WH. Identification and evolutionary analysis of long non-coding RNAs in zebra finch. BMC Genomics 2017; 18:117. [PMID: 28143393 PMCID: PMC5282891 DOI: 10.1186/s12864-017-3506-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/14/2017] [Indexed: 02/06/2023] Open
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.
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Affiliation(s)
- Chih-Kuan Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Sung-Chou Li
- Department of Medical Research, Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Di-Rong Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Chau-Ti Ting
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Life Science & Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 10617, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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