1
|
Chan YF, Lu CW, Kuo HC, Hung CM. A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3 (BETHESDA, MD.) 2024; 14:jkae077. [PMID: 38607414 DOI: 10.1093/g3journal/jkae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/04/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.
Collapse
Affiliation(s)
- Yuan-Fu Chan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
2
|
Dhouailly D. The avian ectodermal default competence to make feathers. Dev Biol 2024; 508:64-76. [PMID: 38190932 DOI: 10.1016/j.ydbio.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
Feathers originate as protofeathers before birds, in pterosaurs and basal dinosaurs. What characterizes a feather is not only its outgrowth, but its barb cells differentiation and a set of beta-corneous proteins. Reticula appear concomitantly with feathers, as small bumps on plantar skin, made only of keratins. Avian scales, with their own set of beta-corneous proteins, appear more recently than feathers on the shank, and only in some species. In the chick embryo, when feather placodes form, all the non-feather areas of the integument are already specified. Among them, midventral apterium, cornea, reticula, and scale morphogenesis appear to be driven by negative regulatory mechanisms, which modulate the inherited capacity of the avian ectoderm to form feathers. Successive dermal/epidermal interactions, initiated by the Wnt/β-catenin pathway, and involving principally Eda/Edar, BMP, FGF20 and Shh signaling, are responsible for the formation not only of feather, but also of scale placodes and reticula, with notable differences in the level of Shh, and probably FGF20 expressions. This sequence is a dynamic and labile process, the turning point being the FGF20 expression by the placode. This epidermal signal endows its associated dermis with the memory to aggregate and to stimulate the morphogenesis that follows, involving even a re-initiation of the placode.
Collapse
Affiliation(s)
- Danielle Dhouailly
- Department of Biology and Chemistry, University Grenoble-Alpes, Institute for Advanced Biosciences, 38700, La Tronche, France.
| |
Collapse
|
3
|
Carron M, Sachslehner AP, Cicekdal MB, Bruggeman I, Demuynck S, Golabi B, De Baere E, Declercq W, Tschachler E, Vleminckx K, Eckhart L. Evolutionary origin of Hoxc13-dependent skin appendages in amphibians. Nat Commun 2024; 15:2328. [PMID: 38499530 PMCID: PMC10948813 DOI: 10.1038/s41467-024-46373-x] [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: 07/02/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Cornified skin appendages, such as hair and nails, are major evolutionary innovations of terrestrial vertebrates. Human hair and nails consist largely of special intermediate filament proteins, known as hair keratins, which are expressed under the control of the transcription factor Hoxc13. Here, we show that the cornified claws of Xenopus frogs contain homologs of hair keratins and the genes encoding these keratins are flanked by promoters in which binding sites of Hoxc13 are conserved. Furthermore, these keratins and Hoxc13 are co-expressed in the claw-forming epithelium of frog toe tips. Upon deletion of hoxc13, the expression of hair keratin homologs is abolished and the development of cornified claws is abrogated in X. tropicalis. These results indicate that Hoxc13-dependent expression of hair keratin homologs evolved already in stem tetrapods, presumably as a mechanism for protecting toe tips, and that this ancestral genetic program was coopted to the growth of hair in mammals.
Collapse
Affiliation(s)
- Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | | | - Munevver Burcu Cicekdal
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Inge Bruggeman
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- VIB-Ugent Center for Inflammation Research, 9000, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Wim Declercq
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- VIB-Ugent Center for Inflammation Research, 9000, Ghent, Belgium
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium.
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria.
| |
Collapse
|
4
|
Sin SYW, Ke F, Chen G, Huang PY, Enbody ED, Karubian J, Webster MS, Edwards SV. Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird. Mol Biol Evol 2024; 41:msae046. [PMID: 38415852 PMCID: PMC10962638 DOI: 10.1093/molbev/msae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.
Collapse
Affiliation(s)
- Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fushi Ke
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Pei-Yu Huang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Erik D Enbody
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael S Webster
- Cornell Lab of Ornithology and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
5
|
Liu TY, Hughes MW, Wang HV, Yang WC, Chuong CM, Wu P. Molecular and Cellular Characterization of Avian Reticulate Scales Implies the Evo-Devo Novelty of Skin Appendages in Foot Sole. J Dev Biol 2023; 11:30. [PMID: 37489331 PMCID: PMC10366821 DOI: 10.3390/jdb11030030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/26/2023] Open
Abstract
Among amniotic skin appendages, avian feathers and mammalian hairs protect their stem cells in specialized niches, located in the collar bulge and hair bulge, respectively. In chickens and alligators, label retaining cells (LRCs), which are putative stem cells, are distributed in the hinge regions of both avian scutate scales and reptilian overlapping scales. These LRCs take part in scale regeneration. However, it is unknown whether other types of scales, for example, symmetrically shaped reticulate scales, have a similar way of preserving their stem cells. In particular, the foot sole represents a special interface between animal feet and external environments, with heavy mechanical loading. This is different from scutate-scale-covered metatarsal feet that function as protection. Avian reticulate scales on foot soles display specialized characteristics in development. They do not have a placode stage and lack β-keratin expression. Here, we explore the molecular and cellular characteristics of avian reticulate scales. RNAscope analysis reveals different molecular profiles during surface and hinge determination compared with scutate scales. Furthermore, reticulate scales express Keratin 15 (K15) sporadically in both surface- and hinge-region basal layer cells, and LRCs are not localized. Upon wounding, the reticulate scale region undergoes repair but does not regenerate. Our results suggest that successful skin appendage regeneration requires localized stem cell niches to guide regeneration.
Collapse
Affiliation(s)
- Tzu-Yu Liu
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Marine Biology and Cetacean Research Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Michael W Hughes
- Institute of Clinical Medicine and Department of Life Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Hao-Ven Wang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Marine Biology and Cetacean Research Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Cheng Yang
- School of Veterinary Medicine, National Taiwan University, Taipei 106216, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University Southern California, Los Angeles, CA 90033, USA
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
6
|
Cooper RL, Santos-Durán G, Milinkovitch MC. Protocol for the rapid intravenous in ovo injection of developing amniote embryos. STAR Protoc 2023; 4:102324. [PMID: 37210721 DOI: 10.1016/j.xpro.2023.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023] Open
Abstract
We present a technique for precise drug delivery into the vascular system of developing amniote embryos via injection into chorioallantoic veins underlying the eggshell membrane. We describe steps for incubating and candling eggs, removing the shell to expose underlying veins, and precise intravenous injection. In addition to chicken embryos, this protocol is applicable to other amniote species that lay hard-shell eggs, including crocodiles and tortoises. This technique is rapid, is reproducible, is of low cost, and will provide an important resource for developmental biologists. For complete details on the use and execution of this protocol, please refer to Cooper & Milinkovitch.1.
Collapse
Affiliation(s)
- Rory L Cooper
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Gabriel Santos-Durán
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Michel C Milinkovitch
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
| |
Collapse
|