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    Characterization of 32 microsatellite loci for the Pacific red snapper, Lutjanus peru, through next generation sequencing

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    Paz-Garcia_Oct2016_clean.pdf
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    Description:
    Final Accepted Manuscript
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    Author
    Paz-García, David A. cc
    Munguía-Vega, Adrián cc
    Plomozo-Lugo, Tomas
    Weaver, Amy Hudson
    Affiliation
    Conservation Genetics Laboratory, School of Natural Resources and the Environment, The University of Arizona
    Issue Date
    2017-04-27
    Keywords
    Population genetics
    Gulf of California
    Marine connectivity
    Pyrosequencing
    Microsatellites
    Lutjanidae
    
    Metadata
    Show full item record
    Publisher
    SPRINGER
    Citation
    Characterization of 32 microsatellite loci for the Pacific red snapper, Lutjanus peru, through next generation sequencing 2017, 44 (2):251 Molecular Biology Reports
    Journal
    Molecular Biology Reports
    Rights
    © Springer Science+Business Media Dordrecht 2017.
    Collection Information
    This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
    Abstract
    We developed a set of hypervariable microsatellite markers for the Pacific red snapper (Lutjanus peru), an economically important marine fish for small-scale fisheries in the west coast of Mexico. We performed shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatic tools to search for perfect microsatellite loci. We selected 66 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from the Gulf of California. We estimated levels of genetic diversity, deviations from linkage and Hardy-Weinberg equilibrium, estimated the frequency of null alleles and the probability of individual identity for the new markers. We reanalyzed 16 loci in 16 individuals to estimate genotyping error rates. Eighteen loci failed to amplify, 16 loci were discarded due to unspecific amplifications and 32 loci (14 tetranucleotide and 18 dinucleotide) were successfully scored. The average number of alleles per locus was 21 (+/- 6.87, SD) and ranged from 8 to 34. The average observed and expected heterozygosities were 0.787 (+/- 0.144 SD, range 0.250-0.935) and 0.909 (+/- 0.122 SD, range 0.381-0.965), respectively. No significant linkage was detected. Eight loci showed deviations from Hardy-Weinberg equilibrium, and from these, four loci showed moderate null allele frequencies (0.104-0.220). The probability of individual identity for the new loci was 1.46(-62). Genotyping error rates averaged 9.58%. The new markers will be useful to investigate patterns of larval dispersal, metapopulation dynamics, fine-scale genetic structure and diversity aimed to inform the implementation of spatially explicit fisheries management strategies in the Gulf of California.
    Note
    12 month embargo; First Online: 27 April 2017
    ISSN
    0301-4851
    1573-4978
    PubMed ID
    28451874
    DOI
    10.1007/s11033-017-4105-4
    Version
    Final accepted manuscript
    Sponsors
    CONACYT [250126]; Walton Family Foundation [2011-1235]; David and Lucile Packard Foundation [2013-39359, 2013-39400, 2015-62798]
    Additional Links
    http://link.springer.com/10.1007/s11033-017-4105-4
    ae974a485f413a2113503eed53cd6c53
    10.1007/s11033-017-4105-4
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