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Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers. Sci Rep 2021; 11:15260. [PMID: 34315937 PMCID: PMC8316385 DOI: 10.1038/s41598-021-93000-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022] Open
Abstract
In order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei's genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.
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Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes. Genes (Basel) 2020; 11:genes11111271. [PMID: 33126655 PMCID: PMC7692064 DOI: 10.3390/genes11111271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.
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Chen B, Li Y, Peng W, Zhou Z, Shi Y, Pu F, Luo X, Chen L, Xu P. Chromosome-Level Assembly of the Chinese Seabass ( Lateolabrax maculatus) Genome. Front Genet 2019; 10:275. [PMID: 31019525 PMCID: PMC6459032 DOI: 10.3389/fgene.2019.00275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- Shenzhen Research Institute of Xiamen University, Shenzhen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Zhao Y, Peng W, Guo H, Chen B, Zhou Z, Xu J, Zhang D, Xu P. Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:45-59. [PMID: 29256104 DOI: 10.1007/s10126-017-9786-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.
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Affiliation(s)
- Yunfeng Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Wenzhu Peng
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Huayang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Baohua Chen
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Zhixiong Zhou
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Dianchang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Peng Xu
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China.
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Wang ZP, Wang D, Wang CL, Xie WJ, Zhu YF, Chen XW. Transcriptome characterization of HPG axis from Chinese sea perch Lateolabrax maculatus. JOURNAL OF FISH BIOLOGY 2017; 91:1407-1418. [PMID: 28913865 DOI: 10.1111/jfb.13459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Here the transcriptome and differential gene expression in the adult brain and gonads of the Chinese sea perch Lateolabrax maculatus were reported. A total of 78 256 909 clean reads were generated from the adult brain, ovary and testis by using the Illumina HiSeq2000 platform and assembled into 274 909 contigs. A total of 31 683 unigenes were annotated based on sequence similarity and 20 702 unigenes were found to exhibit 8237 gene ontology terms and 3888 signal pathways. Transcripts of 26 623 unigenes were present in all of the tissues, whereas pairwise comparisons revealed that 671/367, 496/315 and 1668/580 unigenes were up-down regulated by at least two-fold between the brain and ovary, ovary and testis and brain and testis, respectively. Homology search led to the identification of reproduction-associated genes of the brain-gonad axis, including those involved in sex differentiation and maintenance. The data provided an integrated and comprehensive transcriptome resource for L. maculatus, which could be used for further research on hypothalamus-pituitary-gonad axis gene function, reproduction regulation and sex-biased gene expression.
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Affiliation(s)
- Z P Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - D Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - C L Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - W J Xie
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Y F Zhu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - X W Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
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Liu K, Duan J, Xu D, Zhou Y, Zhang M, Fang D, Xu P. Complete mitochondrial genome of Lateolabrax maculatus. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2510-1. [PMID: 26075475 DOI: 10.3109/19401736.2015.1036253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we sequence the complete mitochondrial genome of Lateolabrax maculatus. This mitochondrial genome is 16,597 bp in length, encoding 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a non-coding control region as found in other vertebrates, with the gene synteny identical to those of typical vertebrates. Control region (D-Loop), of 929 bp in length, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 25.9%, C 29.5%, A 27.3% and G 17.3%, with an AT bias of 53.2%.
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Affiliation(s)
- Kai Liu
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Jinrong Duan
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Dongpo Xu
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Yanfeng Zhou
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Minying Zhang
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Dian Fang
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
| | - Pao Xu
- a Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences , Wuxi , China
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