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Zhang S, Ding J, Han Z, Chen S, Liu Y, He W, He P. Development of SSR markers and genetic diversity analysis based on RAD-seq technology among Chinese populations of Daphnia magna. Mol Biol Rep 2022; 49:4389-4397. [PMID: 35552958 DOI: 10.1007/s11033-022-07274-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/16/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Daphnia magna belongs to the Cladocera order and plays an important role in the aquatic ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. METHODS AND RESULTS 26 novel microsatellite (SSR) markers were developed in an artificially domesticated D. magna and 12 wild D. magna populations using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei's genetic identity (H) ranged from 0.0926 to 0.3462. Shannon's Information index (I) ranged from 0.1333 to 0.4799. Genetic distance and Nei's genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan are relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the D. magna samples into two major groups. CONCLUSIONS These results indicate that the genetic structure of D. magna differs considerably in different regions. Our research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated populations and conservation genetics research.
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Affiliation(s)
- Shengman Zhang
- School of Environment and Chemical Engineering, Shanghai University, Shanghai, 200444, China.,College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.,Water Environment and Ecology Engineering Research Center of Shanghai Institution of Higher Education, Shanghai, 201306, China
| | - Jingxiang Ding
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.,Water Environment and Ecology Engineering Research Center of Shanghai Institution of Higher Education, Shanghai, 201306, China
| | - Zheng Han
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.,Water Environment and Ecology Engineering Research Center of Shanghai Institution of Higher Education, Shanghai, 201306, China
| | - Siwei Chen
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.,Water Environment and Ecology Engineering Research Center of Shanghai Institution of Higher Education, Shanghai, 201306, China
| | - Yuchao Liu
- Shanghai Taihe Water Environment Technology Development Co. Ltd., Shanghai, 200433, China
| | - Wenhui He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China. .,Shanghai Taihe Water Environment Technology Development Co. Ltd., Shanghai, 200433, China.
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China. .,Water Environment and Ecology Engineering Research Center of Shanghai Institution of Higher Education, Shanghai, 201306, China.
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Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844). Mol Biol Rep 2021; 48:6471-6480. [PMID: 34420147 DOI: 10.1007/s11033-021-06653-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described. METHODS AND RESULTS In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (HO) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (HE) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05). CONCLUSIONS These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.
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Zhao N, Guo H, Jia L, Guo B, Zheng D, Liu S, Zhang B. Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes. Genomics 2021; 113:717-726. [PMID: 33535123 DOI: 10.1016/j.ygeno.2021.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023]
Abstract
High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
| | - Haobing Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Biao Guo
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Debin Zheng
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Shanshan Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin 300200, China.
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Mao C, Zhang T, Ren A, Jia X, Lai SJ, Chen SY. Genome-wide SNP discovery and genetic diversity evaluation of Liangshan cattle in China. Anim Biotechnol 2020; 32:671-675. [PMID: 32163006 DOI: 10.1080/10495398.2020.1739061] [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: 10/24/2022]
Abstract
Liangshan cattle are a very small indigenous breed with adult weight of less than 300 Kg and have been mainly distributed in the Liangshan Yi Autonomous Prefecture of Southwestern Sichuan, China. Due to its long-term adaptation to local environments, Liangshan cattle is a valuable genetic resource and should be paid with more attentions. However, the genetic diversity of Liangshan cattle have not been specifically investigated yet, which would be required when designing the appropriate conservation and utilization programs. In this study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to explore a total of 84,854 genome-wide and high-confidence SNPs of Liangshan cattle. All these SNPs were evenly distributed through all chromosomes with an average of 98 SNPs per 1-Mb region. The nucleotide diversity, expected heterozygosity, polymorphism information content of Liangshan cattle were 0.227, 0.223 and 0.183, respectively. Furthermore, there was no obvious difference on the genetic diversity among the three studied geographical populations. In conclusion, we provided a list of SNPs that could be used in the follow-up studies for Liangshan cattle and revealed a relatively high genetic variation in this gene pool.
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Affiliation(s)
- Chuyang Mao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Tao Zhang
- Institute of Animal Husbandry and Veterinary Science of Liangshan Yi Autonomous Prefecture, Xichang, China
| | - Anyong Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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