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Chong Y, Tu X, Lu Y, Gao Z, He X, Hong J, Wu J, Wu D, Xi D, Deng W. Two High-Quality Cygnus Genome Assemblies Reveal Genomic Variations Associated with Plumage Color. Int J Mol Sci 2023; 24:16953. [PMID: 38069278 PMCID: PMC10707585 DOI: 10.3390/ijms242316953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The Cygnus genus features two species, Cygnus olor and Cygnus atratus, that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive. Herein, we present two high-quality genomes for C. olor and C. atratus, procured using the Illumina and Nanopore technologies. The assembled genome of C. olor was 1.12 Gb in size with a contig N50 of 26.82 Mb, while its counterpart was 1.13 Gb in size with a contig N50 of 21.91 Mb. A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, we also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, we demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production. Finally, our findings offer insight into the intricate pattern of pigmentation and the role of polygenes in birds. Furthermore, these two high-quality genome references provide a comprehensive resource and perspective for comparative functional and genetic studies of evolution within the Cygnus genus.
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Affiliation(s)
- Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaoming He
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
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Evident hypopigmentation without other ocular deficits in Dutch patients with oculocutaneous albinism type 4. Sci Rep 2021; 11:11572. [PMID: 34078970 PMCID: PMC8172864 DOI: 10.1038/s41598-021-90896-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
To describe the phenotype of Dutch patients with oculocutaneous albinism type 4 (OCA4), we collected data on pigmentation (skin, hair, and eyes), visual acuity (VA), nystagmus, foveal hypoplasia, chiasmal misrouting, and molecular analyses of nine Dutch OCA4 patients from the Bartiméus Diagnostic Center for complex visual disorders. All patients had severely reduced pigmentation of skin, hair, and eyes with iris transillumination over 360 degrees. Three unrelated OCA4 patients had normal VA, no nystagmus, no foveal hypoplasia, and no misrouting of the visual pathways. Six patients had poor visual acuity (0.6 to 1.0 logMAR), nystagmus, severe foveal hypoplasia and misrouting. We found two novel variants in the SLC45A2 gene, c.310C > T; (p.Pro104Ser), and c.1368 + 3_1368 + 9del; (p.?). OCA4 patients of this Dutch cohort all had hypopigmentation of skin, hair, and iris translucency. However, patients were either severely affected with regard to visual acuity, foveal hypoplasia, and misrouting, or visually not affected at all. We describe for the first time OCA4 patients with an evident lack of pigmentation, but normal visual acuity, normal foveal development and absence of misrouting. This implies that absence of melanin does not invariably lead to foveal hypoplasia and abnormal routing of the visual pathways.
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Okamura K, Suzuki T. Current landscape of Oculocutaneous Albinism in Japan. Pigment Cell Melanoma Res 2020; 34:190-203. [PMID: 32969595 DOI: 10.1111/pcmr.12927] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Abstract
Oculocutaneous albinism (OCA), which is roughly divided into non-syndromic and syndromic OCA, is a group of autosomal recessive disorders caused by mutations in genes associated with pigmentation. Patients with OCA have hypopigmentation and ocular manifestations such as photophobia, amblyopia, and nystagmus. Hermansky-Pudlak syndrome (HPS), the most common syndromic OCA, is characterized by the additional features of a bleeding tendency and other critical systemic comorbidities such as pulmonary fibrosis and immunodeficiency. NGS-based gene analyses have identified several new causative genes for OCA and have detected rare subtypes of OCA with high accuracy including Japanese patients. In our survey of 190 Japanese OCA patients/families, OCA4 is the most common subtype (25.3%) followed by OCA1 (20.0%), HPS1 (14.7%), and OCA2 (8.4%). Similar to the A481T variant in OCA2, which is associated with a mild form of OCA2 and skin color variation, the c.-492_489delAATG variant located in the promoter region of SLC45A2 has been uniquely identified in Japanese patients with a mild form of OCA4. Further, rare OCA subtypes, including OCA3, HPS2, HPS3, HPS4, HPS5, HPS6, and HPS9, have also been identified in Japanese patients. The clinical characteristics and underlying molecular mechanisms of each subtype of OCA are concisely summarized in this review.
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Affiliation(s)
- Ken Okamura
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tamio Suzuki
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
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Hida T, Tsukamoto K, Okura M, Uhara H. Homozygous promoter variant of SLC45A2 causes diverse hair color and patterns. J Dermatol 2020; 47:e351-e352. [PMID: 32686196 DOI: 10.1111/1346-8138.15509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tokimasa Hida
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Katsuhiko Tsukamoto
- Department of Dermatology, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Masae Okura
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hisashi Uhara
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Okamura K, Hayashi M, Abe Y, Kono M, Nakajima K, Aoyama Y, Nishigori C, Ishimoto H, Ishimatsu Y, Nakajima M, Hozumi Y, Suzuki T. NGS‐based targeted resequencing identified rare subtypes of albinism: Providing accurate molecular diagnosis for Japanese patients with albinism. Pigment Cell Melanoma Res 2019; 32:848-853. [DOI: 10.1111/pcmr.12800] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/26/2019] [Accepted: 05/17/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Ken Okamura
- Department of Dermatology, Faculty of Medicine Yamagata University Yamagata Japan
| | - Masahiro Hayashi
- Department of Dermatology, Faculty of Medicine Yamagata University Yamagata Japan
| | - Yuko Abe
- Department of Dermatology, Faculty of Medicine Yamagata University Yamagata Japan
| | - Michihiro Kono
- Department of Dermatology Nagoya University Graduate School of Medicine Nagoya Japan
| | - Kimiko Nakajima
- Department of Dermatology, Kochi Medical School Kochi University Kochi Japan
| | - Yumi Aoyama
- Department of Dermatology Kawasaki Medical School Kurashiki Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related Kobe University Graduate School of Medicine Kobe Japan
| | - Hiroshi Ishimoto
- Department of Respiratory Medicine Nagasaki University Graduate School of Biomedical Sciences Nagasaki Japan
| | - Yuji Ishimatsu
- Department of Nursing Nagasaki University Graduate School of Biomedical Sciences Nagasaki Japan
| | - Mika Nakajima
- Department of Pediatrics Hakodate Central General Hospital Hakodate Japan
| | - Yutaka Hozumi
- Department of Dermatology, Faculty of Medicine Yamagata University Yamagata Japan
| | - Tamio Suzuki
- Department of Dermatology, Faculty of Medicine Yamagata University Yamagata Japan
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Okamura K, Abe Y, Hayashi M, Saito T, Nagatani K, Tanoue T, Wataya-Kaneda M, Hozumi Y, Suzuki T. Impact of a 4-bp deletion variant (rs984225803) in the promoter region of SLC45A2 on color variation among a Japanese population. J Dermatol 2019; 46:e295-e296. [PMID: 30809845 DOI: 10.1111/1346-8138.14831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ken Okamura
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Yuko Abe
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masahiro Hayashi
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Toru Saito
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Kei Nagatani
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Toshihide Tanoue
- Division of Dermatology, Tanoue Dermatology Clinic, Kumamoto, Japan
| | - Mari Wataya-Kaneda
- Department of Dermatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yutaka Hozumi
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Tamio Suzuki
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
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