Development of 39 polymorphic microsatellite markers for the jumbo squid Dosidicus gigas using Illumina paired-end seque
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MICROSATELLITE LETTERS
Development of 39 polymorphic microsatellite markers for the jumbo squid Dosidicus gigas using Illumina paired-end sequencing Lianwei Liu • Xinjun Chen • Qianghua Xu Siquan Tian • Bilin Liu
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Received: 19 February 2014 / Accepted: 24 March 2014 Springer Science+Business Media Dordrecht 2014
Abstract Dosidicus gigas is an abundant squid species supporting one of the most important fisheries in the Eastern Pacific Ocean. Assessment and management of the fishery requires reliable information on the population’s genetic structure. In this study, we isolated and characterized 39 novel polymorphic microsatellite loci for D. gigas using Illumina paired-end sequencing. Loci were screened in 20 individuals from the Eastern Pacific Ocean. The number of alleles per locus ranged from 4 to 26 (mean = 14.72). The observed heterozygosity ranged from 0.150 to 0.950 (mean = 0.604), and the expected heterozygosity ranged from 0.487 to 0.972 (mean = 0.872). The polymorphic information content ranged from 0.440 to 0.945, with a mean of 0.836. These microsatellite loci are expected to be useful for further studies of genetic diversity and genetic structure of D. gigas. Keywords Dosidicus gigas Microsatellite Illumina paired-end sequencing Genetic structure The jumbo flying squid, Dosidicus gigas, is native to the eastern Pacific Ocean and occurs over a wide geographic
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0179-7) contains supplementary material, which is available to authorized users. L. Liu X. Chen (&) Q. Xu S. Tian B. Liu College of Marine Sciences, Shanghai Ocean University, Hucheng Ring Road 999, Lingang New City, Shanghai 201306, China e-mail: [email protected] X. Chen Q. Xu S. Tian B. Liu The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Hucheng Ring Road 999, Shanghai 201306, China
range that extends from California (37–40N) through to southern Chile (45–47S), stretching to the west from the coast to a maximum of 125–140W at the Equator (Nigmatullin et al. 2001). It supports an important fishery in the Gulf of California and in coastal and oceanic waters of Peru and Chile (Anderson and Rodhouse 2001). D. gigas is short-lived, and population fluctuations are likely to occur in response to environmental variability (Waluda et al. 2006). Consequently, it is extremely urgent to define the genetic structure of D. gigas. Microsatellites are tandemly repeated motifs of 1–6 bases distributed randomly in genomes, which show extensive levels of intraspecific polymorphisms (Zane et al. 2002). In this study, we developed 39 polymorphic microsatellite markers for D. gigas using Illumina paired-end sequencing that can be used in future population genetics studies. No less than 3 lg of genomic DNA was extracted from 10 D. gigas individual species obtained from the oceanic waters of Peru using the Genomic DNA Isolation Kit (FOREGENE CO., LTD). An Illumina paired-end shotgun library
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