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Zhang J, Qi J, Shi F, Pan H, Liu M, Tian R, Geng Y, Li H, Qu Y, Chen J, Seim I, Li M. Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis. iScience 2020; 23:101267. [PMID: 32593955 PMCID: PMC7327861 DOI: 10.1016/j.isci.2020.101267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/28/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
Salangids, known as Asian icefishes, represent a peculiar radiation within the bony fish order Protacanthopterygii where adult fish retain larval characteristics such as transparent and miniaturized bodies and a cartilaginous endoskeleton into adulthood. Here, we report a de novo genome of Protosalanx chinensis, the most widely distributed salangid lineage. The P. chinensis genome assembly is more contiguous and complete than a previous assembly. We estimate that P. chinensis, salmons, trouts, and pikes diverged from a common ancestor 185 million years ago. A juxtaposition with other fish genomes revealed loss of the genes encoding ectodysplasin-A receptor (EDAR), SCPP1, and four Hox proteins and likely lack of canonical fibroblast growth factor 5 (FGF5) function. We also report genomic variations of P. chinensis possibly reflecting the immune system repertoire of a species with a larval phenotype in sexually mature individuals. The new Asian icefish reference genome provides a solid foundation for future studies.
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Affiliation(s)
- Jie Zhang
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.
| | - Jiwei Qi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Fanglei Shi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Pan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Huaying Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yujie Qu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource, Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China.
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD 4102, Australia.
| | - Ming Li
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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