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Liu B, Zhou Z, Bai Y, Yang J, Shi Y, Pu F, Xu P. Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia. Front Genet 2021; 12:625600. [PMID: 33692829 PMCID: PMC7937929 DOI: 10.3389/fgene.2021.625600] [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: 11/03/2020] [Accepted: 01/07/2021] [Indexed: 12/31/2022] Open
Abstract
As a typical marine adaptive radiation species, most Takifugu species are widely distributed in East Asian offshore, which have diversified morphological characteristics and different ecological habits. The phylogenetic relationship and population structure of the Takifugu species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of Takifugu genus, explore the introgression and natural hybridization between different Takifugu species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 Takifugu samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between Takifugu bimaculatus and Takifugu flavidus, Takifugu oblongus, and Takifugu niphobles, Takifugu rubripes, and Takifugu obscurus, Takifugu xanthoptreus, and Takifugu ocellatus. Further admixture analysis indicated the divergence of T. obscurus population and the bidirectional gene flow between T. bimaculatus and T. flavidus. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between T. bimaculatus and T. flavidus at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of syt1, zar1 and tgfbr1 related to the semilunar reproduction rhythm in T. niphobles, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of T. niphobles specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For Takifugu species, our research provides reliable genetic resources and results for the phylogeny, introgression, hybridization and adaptive evolution, and could be used as a guide for the formulation of the protection and proliferation release policies.
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Affiliation(s)
- Bo Liu
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Junyi Yang
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yue Shi
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen, China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Dou D, Wang X, Zhu H, Bao Y, Wang Y, Cui J, Meng X, Zhu Y, Qiu X. The complete mitochondrial genome of the hybrid of Takifugu obscurus (♀) × Takifugu rubripes (♂). Mitochondrial DNA B Resour 2019; 4:3196-3197. [PMID: 33365916 PMCID: PMC7707280 DOI: 10.1080/23802359.2019.1669082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/16/2019] [Indexed: 10/27/2022] Open
Abstract
The complete mitochondrial genome of the hybrid of Takifugu obscurus (♀) × Takifugu rubripes (♂) was sequenced and characterized in this study. The hybrid mitochondrial DNA, with a total length of 16,443 bp, contain 37 genes, including 13 protein-coding genes, 22 tRNAs genes, and 2 rRNA gene. There are two noncoding regions: the origin of light-strand replication (OL) and control region (D-loop). The complete mitochondrial genome of the hybrid of T. obscurus (♀) × T. rubripes (♂) provides data for studies on genetic diversity and species identification among Takifugu.
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Affiliation(s)
- Dongyu Dou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Xiuli Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Haoyong Zhu
- Jiangsu Zhongyang Group Company Limited, Haian, Jiangsu, China
| | - Yulong Bao
- Dalian Tianzheng Industrial Co. Ltd, Dalian, Liaoning, China
| | - Yaohui Wang
- Jiangsu Zhongyang Group Company Limited, Haian, Jiangsu, China
| | - Jun Cui
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Xuesong Meng
- Dalian Tianzheng Industrial Co. Ltd, Dalian, Liaoning, China
| | - Yongxiang Zhu
- Jiangsu Zhongyang Group Company Limited, Haian, Jiangsu, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
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Jiang H, Liu B, Lü Z, Liu L, Gong L. The complete mitochondrial genome of Lagocephalus sceleratus (Tetraodontiformes; Tetraodontidae) and phylogenetic studies of Tetraodontidae. Mitochondrial DNA B Resour 2018; 3:866-867. [PMID: 33474347 PMCID: PMC7800810 DOI: 10.1080/23802359.2018.1502633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 11/23/2022] Open
Abstract
The complete mitochondrial genome sequence of Lagocephalus sceleratus was determined. The complete mitochondrial genome was 16,444 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding region (the control region and the origin of light strand replication). The overall base composition was A 27.59%, C 31.43%, G 17.12%, T 23.85%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. Additionally, the phylogenetic relationship of 37 Tetraodontidae species based on the complete genome was analyzed, and the result showed that L. sceleratus was clustered with other Lagocephalus species. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Tetraodontidae.
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Affiliation(s)
- Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, South Haida Road, Dinghai District
- Zhoushan 316022, Zhejiang, China; 2 National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, People’s Republic of China.
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, South Haida Road, Dinghai District
- Zhoushan 316022, Zhejiang, China; 2 National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, People’s Republic of China.
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, South Haida Road, Dinghai District
- Zhoushan 316022, Zhejiang, China; 2 National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, People’s Republic of China.
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, South Haida Road, Dinghai District
- Zhoushan 316022, Zhejiang, China; 2 National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, People’s Republic of China.
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, South Haida Road, Dinghai District
- Zhoushan 316022, Zhejiang, China; 2 National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, People’s Republic of China.
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