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

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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.

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Acknowledgements

We would like to acknowledge Mariana Walther, Juan Leonardo Lucero Cuevas (Tito) and Jose Amador Gutierrez (Pepe) for their assistance with acquiring samples in the field, and Ollin Gonzalez-Cuellar for helping with logistics during the project. Alexander Ochoa, Karla Vargas, Jose Francisco Dominguez-Contreras (Borre), Geraldine Parra and Stacy L. Sotak help us at various stages during microsatellite genotyping. DAPG received a CONACYT fellowship (250126). This work was funded by The Walton Family Foundation grant # 2011-1235 and The David and Lucile Packard Foundation grants #2013-39359, #2013-39400, #2015-62798. We also thank two anonymous reviewers for helpful comments that improved this manuscript.

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Authors and Affiliations

  1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA

    David A. Paz-García

  2. Laboratorio de Necton y Ecología de arrecifes. Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional, 195, Col. Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, Mexico

    David A. Paz-García

  3. PANGAS Science Coordination, Comunidad y Biodiversidad A.C., Guaymas, Sonora, Mexico

    Adrián Munguía-Vega

  4. Conservation Genetics Laboratory, School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ, USA

    Adrián Munguía-Vega

  5. @Genetics Lab., La Paz, Baja California Sur, Mexico

    Adrián Munguía-Vega

  6. Sociedad de Historia Natural Niparaja A.C., La Paz, Baja California Sur, Mexico

    Tomas Plomozo-Lugo & Amy Hudson Weaver

Authors
  1. David A. Paz-García
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  2. Adrián Munguía-Vega
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  3. Tomas Plomozo-Lugo
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  4. Amy Hudson Weaver
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Corresponding author

Correspondence to Adrián Munguía-Vega.

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Paz-García, D.A., Munguía-Vega, A., Plomozo-Lugo, T. et al. Characterization of 32 microsatellite loci for the Pacific red snapper, Lutjanus peru, through next generation sequencing. Mol Biol Rep 44, 251–256 (2017). https://doi.org/10.1007/s11033-017-4105-4

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  • DOI: https://doi.org/10.1007/s11033-017-4105-4

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