Development and characterization of thirty-three microsatellite markers for the Patagonian sprat, Sprattus fuegensis (Jenyns, 1842), using paired-end Illumina shotgun sequencing

Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Canales‐Aguirre, Cristian B.; Love, Cara N.; Jones, Kenneth L.; Lance, Stacey L.

doi:10.1007/s12686-014-0281-x

Cited by 3 publications

(5 citation statements)

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“…We used eight tetranucleotide microsatellites with loci described for S . fuegensis by Ferrada-Fuentes et al [ 63 ] (i.e. Spfu_6, Spfu_9, Spfu_29, Spfu_30, Spfu_42, Spfu_44, Spfu_45, and Spfu_48).…”

Section: Methodsmentioning

confidence: 99%

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Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

et al. 2016

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Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA.

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Section: Methodsmentioning

confidence: 99%

“…Spfu_6, Spfu_9, Spfu_29, Spfu_30, Spfu_42, Spfu_44, Spfu_45, and Spfu_48). These loci were amplified following the protocol described previously by Ferrada-Fuentes et al [ 63 ] and in the PCR procedures we included both positive and negative controls. The PCR products were run on an ABI-3130xl sequencer and sized with Naurox size standard.…”

Section: Methodsmentioning

confidence: 99%

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

et al. 2016

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“…The Atlantic stocks are monitored via scientific surveys (Casarsa et al 2019). It occurs in the marine protected area known as Bahia Tictoc in Corcovado Gulf, Chile (Ferrada-Fuentes et al 2014) and the Namuncurá Marine Protected Area-Burdwood Bank located on the Argentinian shelf (Alonso et al 2018).…”

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confidence: 99%

Sprattus fuegensis: Buratti, C., Díaz de Astarloa, J., Hüne, M., Irigoyen, A., Landaeta, M., Riestra, C., Vieira, J.P. & Di Dario, F.

Buratti¹,

Astarloa²,

Hüne³

et al. 2019

IUCN Red List of Threatened Species

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This coastal, pelagic species is widely distributed in the southwestern Atlantic and southeastern Pacific. It is short-lived and has an estimated generation length of 3-4 years. It is targeted by commercial, artisanal fisheries in the northern part of its range in Chile. Total biomass has declined by about 40% over the past three generation lengths, or since 2006, in the Lakes Region of Chile, and that stock is considered overfished. However, it is not targeted elsewhere in its range at this time, including in the area that contains the largest proportion of its global population. Fishing activity is not expected to be driving global-level declines approaching a Near Threatened or threatened level at this time; therefore, it is listed as Least Concern. However, fishing effort may expand further south where it remains abundant, and this is a concern.

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“…Microsatellite loci are widely used to understand how the genetic diversity of marine organisms is distributed along the geographic space. In addition, this information can be useful for management of marine resources (Canales-Aguirre et al, 2010a, 2010b, 2016Galleguillos et al, 2011Galleguillos et al, , 2012Ferrada-Fuentes et al, 2014). Traditional Short Sequence Repeat (SSR) development is time-consuming and involves laborious iterations of genomic DNA library screening with SSR probes required to isolate microsatellite-containing sequences (Castoe et al, 2012).…”

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confidence: 99%

“…Traditional Short Sequence Repeat (SSR) development is time-consuming and involves laborious iterations of genomic DNA library screening with SSR probes required to isolate microsatellite-containing sequences (Castoe et al, 2012). Next-generation sequencing technologies are remarkably welldeveloped and are widely used for genome sequencing, transcriptome sequencing, and genome deepsequencing in animals (Ferrada-Fuentes et al, 2014;Plough & Marko, 2014). The use of new technologies, like Illumina, 454 or SOLiD sequencing, to create and…”

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confidence: 99%

Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing

Ferrada-Fuentes

Galleguillos

Canales‐Aguirre

et al. 2018

lajar

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The anchovy, Engraulis ringens, is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele's presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management.

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Development and characterization of thirty-three microsatellite markers for the Patagonian sprat, Sprattus fuegensis (Jenyns, 1842), using paired-end Illumina shotgun sequencing

Cited by 3 publications

References 5 publications

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

Sprattus fuegensis: Buratti, C., Díaz de Astarloa, J., Hüne, M., Irigoyen, A., Landaeta, M., Riestra, C., Vieira, J.P. & Di Dario, F.

Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing

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