FishPIE: A universal phylogenetically informative exon markers set for ray-finned fishes
Xidong Mu,
Yexin Yang,
Jinhui Sun,
Yi liu,
Meng Xu,
Changwei Shao,
Ka Hou Chu,
Wei Li,
Chao Liu,
Dangen Gu,
Miao Fang,
Chi Zhang,
Fei Liu,
Hongmei Song,
Xuejie Wang,
Jiehu Chen,
Ka Yan Ma
Affiliations
Xidong Mu
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Corresponding author
Yexin Yang
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Jinhui Sun
College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
Yi liu
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Meng Xu
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Changwei Shao
Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
Ka Hou Chu
Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
Wei Li
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou 510380, China
Chao Liu
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Dangen Gu
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Miao Fang
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Chi Zhang
Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 510006, China
Fei Liu
Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 510006, China
Hongmei Song
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China
Xuejie Wang
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
Jiehu Chen
Science Corporation of Gene (SCGene), Guangzhou 510000, China
Ka Yan Ma
State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Sun Yat-sen University, Guangzhou 510006, China; Corresponding author
Summary: Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life.
