Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis

Jie Zhang; Jiwei Qi; Fanglei Shi; Huijuan Pan; Meng Liu; Ran Tian; Yuepan Geng; Huaying Li; Yujie Qu; Jinping Chen; Inge Seim; Ming Li

doi:10.1016/j.isci.2020.101267

Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis

iScience. 2020 Jul 24;23(7):101267. doi: 10.1016/j.isci.2020.101267. Epub 2020 Jun 14.

Authors

Jie Zhang¹, Jiwei Qi², Fanglei Shi³, Huijuan Pan⁴, Meng Liu⁵, Ran Tian⁶, Yuepan Geng⁶, Huaying Li⁵, Yujie Qu⁵, Jinping Chen⁷, Inge Seim⁸, Ming Li⁹

Affiliations

¹ Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China. Electronic address: zhangjie@ioz.ac.cn.
² Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.
³ 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.
⁴ School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
⁵ Novogene Bioinformatics Institute, Beijing 100083, China.
⁶ Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
⁷ 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. Electronic address: chenjp@giabr.gd.cn.
⁸ 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. Electronic address: inge@seimlab.org.
⁹ 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. Electronic address: lim@ioz.ac.cn.

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.

Keywords: Biological Sciences; Evolutionary Biology; Genomics.