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Nazia AK, Siti Azizah MN. Isolation of microsatellites in the bighead catfish, Clarias macrocephalus and cross-amplification in selected Clarias species. Mol Biol Rep 2014; 41:1207-13. [PMID: 24381108 DOI: 10.1007/s11033-013-2965-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
Abstract
The present study documents the isolation of eight polymorphic microsatellite markers from the bighead catfish, Clarias macrocephalus and cross-amplification in two other catfish species. The number of alleles per locus in C. macrocephalus ranged from 2 to 21. The most polymorphic locus was NCm-G12 with 21 alleles while the least polymorphic locus was NCm-H2 with only two alleles. Locus NCm-F8 significantly deviated from Hardy-Weinberg equilibrium (P value <0.05) after Bonferroni correction. Linkage disequilibrium was non-significant in all loci comparisons. The observed and expected heterozygosities varied from 0.033 to 0.967 and from 0.033 to 0.942, respectively. Mean polymorphic information content for the eight loci was 0.765. Cross-amplification was successfully performed with two other catfish species, C. batrachus and C. meladerma for all eight loci. Locus NCm-D8 was monomorphic in both species while NCm-F8 was monomorphic only in C. batrachus. These newly developed markers would be useful for better management and conservation of the economically important C. macrocephalus species.
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Affiliation(s)
- A K Nazia
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia,
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Konopiński MK, Amirowicz A, Kotlík P, Kukuła K, Bylak A, Pekarik L, Šediva A. Back from the brink: the Holocene history of the Carpathian barbel Barbus carpathicus. PLoS One 2013; 8:e82464. [PMID: 24349291 PMCID: PMC3861402 DOI: 10.1371/journal.pone.0082464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
As a result of specific adaptations and habitat preferences strongly rheophilic fish species may show high levels of endemism. Many temperate rheophilic fish species were subjected to a series of range contractions during the Pleistocene, and then successfully expanded during the Holocene, colonising previously abandoned areas. The Carpathian barbel (Barbus carpathicus Kotlík, Tsigenopoulos, Ráb et Berrebi 2002) occurs in the montane streams in three basins of the main Central European rivers in the northern part of the Carpathian range. We used genetic variation within 3 mitochondrial and 9 microsatellite loci to determine a pattern of postglacial expansion in B. carpathicus. We found that overall genetic variation within the species is relatively low. Estimate of time to the most recent common ancestor (tMRCA) of mitochondrial sequences falls within the Holocene. The highest levels of genetic variation found in upper reaches of the Tisa river in the Danube basin suggest that glacial refugia were located in the south-eastern part of the species range. Our data suggest that the species crossed different watersheds at least six times as three genetically distinct groups (probably established in different expansion episodes) were found in northern part of the species range. Clines of genetic variation were observed in both the Danube and Vistula basins, which probably resulted from subsequent bottlenecks while colonizing successive habitats (south eastern populations) or due to the admixture of genetically diverse individuals to a previously uniform population (Vistula basin). Therefore, B. carpathicus underwent both demographic breakdowns and expansions during the Holocene, showing its distribution and demography are sensitive to environmental change. Our findings are important in the light of the current human-induced habitats alterations.
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Affiliation(s)
- Maciej K. Konopiński
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
- * E-mail:
| | - Antoni Amirowicz
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Petr Kotlík
- Institute of Animal Physiology and Genetics AS CR, Liběchov, Czech Republic
| | - Krzysztof Kukuła
- University of Rzeszów, Department of Environmental Biology, Rzeszów, Poland
| | - Aneta Bylak
- University of Rzeszów, Department of Environmental Biology, Rzeszów, Poland
| | - Ladislav Pekarik
- Institut of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Šediva
- Institut of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
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Nagpure NS, Rashid I, Pati R, Pathak AK, Singh M, Singh SP, Sarkar UK. FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent. BMC Genomics 2013; 14:630. [PMID: 24047532 PMCID: PMC3852227 DOI: 10.1186/1471-2164-14-630] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/11/2013] [Indexed: 11/17/2022] Open
Abstract
Background Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. Description FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. Conclusions FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.
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Affiliation(s)
- Naresh Sahebrao Nagpure
- Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow 226002, India.
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Kaczmarczyk D. Cross-species amplification of selected zebrafish, central stoneroller, and finescale dace microsatellites in lake minnow populations. GENETICS AND MOLECULAR RESEARCH 2013; 12:154-9. [PMID: 23408401 DOI: 10.4238/2013.january.24.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fifteen sets of PCR primers designed for the amplification of microsatellite loci from Danio rerio and Phoxinus neogaeus Campostoma DNA that have been proven applicable for molecular studies of several species of cyprinids were tested for amplification of microsatellites from lake minnow DNA. The samples were taken from 298 fish inhabiting 6 distinct populations located in Poland, and DNA was extracted from dried fin clips. There were 6 sets of primer loci that were identified as useful for amplification of microsatellites from lake minnow DNA, which were polymorphic and could be applied in population genetics of this species. Three other sets of primers provided PCR products with a considerable number of stutter bands obscuring the identity of true microsatellite alleles. The amplification of lake minnow microsatellites using the 6 remaining primer sets was unsuccessful.
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Affiliation(s)
- D Kaczmarczyk
- Department of Environmental Biotechnology, University of Warmia and Mazury, Olsztyn, Poland.
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Singh RK, Lal KK, Mohindra V, Punia P, Sah RS, Kumar R, Gupta A, Das R, Lakra WS, Ayyappan S. Genetic diversity of Indian Major Carp, Labeo calbasu (Hamilton, 1822) populations inferred from microsatellite loci. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ji P, Zhang Y, Li C, Zhao Z, Wang J, Li J, Xu P, Sun X. High throughput mining and characterization of microsatellites from common carp genome. Int J Mol Sci 2012; 13:9798-9807. [PMID: 22949831 PMCID: PMC3431829 DOI: 10.3390/ijms13089798] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/08/2012] [Accepted: 07/24/2012] [Indexed: 01/14/2023] Open
Abstract
In order to supply sufficient microsatellite loci for high-density linkage mapping, whole genome shotgun (WGS) sequences of the common carp (Cyprinus carpio) were assembled and surveyed for microsatellite identification. A total of 79,014 microsatellites were collected which were harbored in 68,827 distinct contig sequences. These microsatellites were characterized in the common carp genome. Information of all microsatellites, including previously published BAC-based microsatellites, was then stored in a MySQL database, and a web-based database interface (http://genomics.cafs.ac.cn/ssrdb) was built for public access and download. A total of 3,110 microsatellites, including 1,845 from WGS and 1,265 from BAC end sequences (BES), were tested and genotyped on a mapping family with 192 individuals. A total of 963 microsatellites markers were validated with polymorphism in the mapping family. They will soon be used for high-density linkage mapping with a vast number of polymorphic SNP markers.
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Affiliation(s)
- Peifeng Ji
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Yan Zhang
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Chao Li
- Heilongjiang Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; E-Mail:
| | - Zixia Zhao
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Jian Wang
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Jiongtang Li
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Peng Xu
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
| | - Xiaowen Sun
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails: (P.J.); (Y.Z.); (Z.Z.); (J.W.); (J.L.)
- Heilongjiang Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; E-Mail:
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Zhang F, Duan Y, Cao S, Wang J, Tan D. High genetic diversity in population of Lepturichthys fimbriata from the Yangtze River revealed by microsatellite DNA analysis. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-011-4704-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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King TL, Eackles MS, Chapman DC. Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-010-9285-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang SH, Zhao QP, Jiao R, Gao Q, Nie P. Identification of Polymorphic Microsatellites for the Intermediate HostOncomelania hupensisofSchistosoma japonicumin China. MALACOLOGIA 2010. [DOI: 10.4002/040.053.0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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CHENG L, LIU L, YU X, TONG J. Sixteen polymorphic microsatellites in bighead carp (Aristichthys nobilis) and cross-amplification in silver carp (Hypophthalmichthys molitrix). Mol Ecol Resour 2008; 8:656-8. [DOI: 10.1111/j.1471-8286.2007.02037.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Liao M, Zhang L, Yang G, Zhu M, Wang D, Wei Q, Zou G, Chen D. Development of silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) genetic maps using microsatellite and AFLP markers and a pseudo-testcross strategy. Anim Genet 2007; 38:364-70. [PMID: 17614988 DOI: 10.1111/j.1365-2052.2007.01617.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) are two of the four most important pond-cultured fish species inhabiting the major river basins of China. In the present study, genetic maps of silver carp and bighead carp were constructed using microsatellite and AFLP markers and a two-way pseudo-testcross strategy. To create the maps, 60 individuals were obtained from a cross of a single bighead carp (female) and a single silver carp (male). The silver carp map consisted of 271 markers (48 microsatellites and 223 AFLPs) that were assembled into 27 linkage groups, of which 22 contained at least four markers. The total length of the silver carp map was 952.2 cM, covering 82.8% of the estimated genome size. The bighead carp map consisted of 153 markers (27 microsatellites and 126 AFLPs) which were organized into 30 linkage groups, of which 19 contained at least four markers. The total length of the bighead carp map was 852.0 cM, covering 70.5% of the estimated genome size. Eighteen microsatellite markers were common to both maps. These maps will contribute to discovery of genes and genetic regions controlling traits in the two species of carp.
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Affiliation(s)
- M Liao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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Carreras-Carbonell J, Macpherson E, Pascual M. Utility of pairwise mtDNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9322-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xiao-Gu Z, Jin-Gou T, Bang-Xi X. Applications of microsatellite markers in studies of genetics and breeding of fish. ACTA ACUST UNITED AC 2007. [DOI: 10.1079/cjb2006104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
AbstractThe microsatellite, or short sequence repeat (SSR), is a powerful genetic marker, useful in many areas of fish genetics and breeding. Polymorphic microsatellite loci have been frequently applied to the analysis of genetic diversity, population genetic structure, and genomic mapping. These co-dominant markers have also been applied to the classification and systematics, parentage identification, germplasm conservation, and breeding programme of food fish.
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LIAO MEIJIE, YANG GUANPIN, WANG XIAOCHEN, WANG DENGQIANG, ZOU GUIWEI, WEI QIWEI. Development of microsatellite DNA markers of silver carp (Hypophthalmichthys molitrix) and their cross-species application in bighead carp (Aristichthys nobilis). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01542.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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GHEYAS AA, CAIRNEY M, GILMOUR AE, SATTAR MA, DAS TK, McANDREW BJ, PENMAN DJ, TAGGART JB. Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross-amplification in other cyprinid species. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01288.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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