title: The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry.
abstract: Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation. The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways. We demonstrate that retinoic acid is critical in establishing asymmetric pigmentation and, via cross-talk with thyroid hormones, in modulating eye migration. The unexpected expression of the visual opsins from the phototransduction pathway in the skin translates illumination differences and generates retinoic acid gradients that underlie the generation of asymmetry. Identifying the genetic underpinning of this unique developmental process answers long-standing questions about the evolutionary origin of asymmetry, but it also provides insight into the mechanisms that control body shape in vertebrates.
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Changwei
authors.initials: C
authors.lastname: Shao
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Baolong
authors.initials: B
authors.lastname: Bao
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Xie
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Xinye
authors.initials: X
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Jia
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qiulin
authors.initials: Q
authors.lastname: Yao
authors.affiliation: Department of Biological Sciences, George Washington University, Washington, DC, USA.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Ortí
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Wenhui
authors.initials: W
authors.lastname: Li
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Xihong
authors.initials: X
authors.lastname: Li
authors.affiliation: National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway.|Department of Biology, University of Bergen, Bergen, Norway.
authors.forename: Kristin
authors.identifier: 0000-0002-8302-3827
authors.initials: K
authors.lastname: Hamre
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Xu
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Fangyuan
authors.initials: F
authors.lastname: Chen
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Tian
authors.affiliation: St. Lawrence University, Biology Department, Canton, New York, USA.
authors.forename: Alex M
authors.initials: AM
authors.lastname: Schreiber
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Na
authors.initials: N
authors.lastname: Wang
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Fen
authors.initials: F
authors.lastname: Wei
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jilin
authors.identifier: 0000-0002-9976-1605
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Zhongdian
authors.initials: Z
authors.lastname: Dong
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Gao
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Junwei
authors.identifier: 0000-0002-9143-9881
authors.initials: J
authors.lastname: Gai
authors.affiliation: Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Sakamoto
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Sudong
authors.initials: S
authors.lastname: Mo
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Yunji
authors.initials: Y
authors.lastname: Xiu
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Yangzhen
authors.initials: Y
authors.lastname: Li
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Wenteng
authors.initials: W
authors.lastname: Xu
authors.affiliation: The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Shi
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Centro de Ciências do Mar (CCMAR), Comparative Endocrinology and Integrative Biology, Universidade do Algarve, Faro, Portugal.|College of Fisheries and Life Science, Shanghai Ocean University, Ministry of Education, Shanghai, China.
authors.forename: Deborah M
authors.identifier: 0000-0003-1366-0246
authors.initials: DM
authors.lastname: Power
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Qingyin
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Physiologische Chemie, University of Würzburg, Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.|Institute for Advanced Studies, Texas A&M University, College Station, Texas, USA.
authors.forename: Manfred
authors.initials: M
authors.lastname: Schartl
authors.affiliation: Yellow Sea Fisheries Research Institute, CAFS, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.|Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Songlin
authors.initials: S
authors.lastname: Chen
mesh_terms: D000818:Animals; D005075:Biological Evolution; D029941:Fish Proteins / Q000235:genetics; D005432:Flounder / Q000033:anatomy & histology* / Q000235:genetics* / Q000254:growth & development; D016678:Genome; D008675:Metamorphosis, Biological / Q000235:genetics*; D013963:Thyroid Hormones / Q000378:metabolism*; D059467:Transcriptome; D014212:Tretinoin / Q000378:metabolism*
chemical_list: D029941:Fish Proteins; D013963:Thyroid Hormones; D014212:Tretinoin