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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Mar. Sci. | doi: 10.3389/fmars.2019.00720

DE NOVO ASSEMBLY AND CHARACTERIZATION OF PATAGONIAN TOOTHFISH TRANSCRIPTOME AND DEVELOP OF EST-SSR MARKERS FOR POPULATION GENETICS

 Jorge Touma1, 2, Killen K. García1, Scarleth Bravo1, Francisco Leiva1, Javier Moya3,  Alberto Reyes3 and  Rodrigo Vidal1*
  • 1Universidad de Santiago de Chile, Chile
  • 2Diego Portales University, Chile
  • 3Other, Chile

Patagonian toothfish (Dissostichus eleginoides) is a hefty notothenioid fish and a key species within the marine ecosystem with a high migratory capacity across sub-Antarctic and south American Pacific oceans. Transcriptome characterization and molecular markers associated with micro and macro-evolutionary studies are not available, which in turn limits the gain of knowledge about the genetic basis of this species. Therefore, in the present study, a de novo transcriptome from eight tissue and an embryonic state of Patagonian toothfish was developed, using the Illumina Hiseq 4000 platform. A total of 233,424 superTranscripts were assembled and 37,446 annotated against public databases. Moreover, we identified 71,107 expressed sequence tag-simple sequence repeats (EST-SSRs), with an average number of 0.3 SSRs per superTranscripts and one SSR per 1.12kB. The most abundant SSR type was repeated dinucleotide (53.67%), followed by trinucleotide (13.73%) repeats. From the total of EST-SSRs identified, 34,196 primer pairs were properly designed and a subset of twenty-five immune loci were selected for its evaluation as potential EST-SSR population markers. Of this subset, eleven proved to have good technical features and were evaluated in 64 animals from four Patagonian toothfish populations. A number of 63 alleles were identified, with a mean of 4.9 alleles per locus and a polymorphism information content ranging from 0.224 to 0.591, with a mean of 0.50. Significant (FST, range 0.082-0.117 and G´ST, range 0.069-0.291) genetic differentiation (P<0.05) was determined among the populations analyzed. Therefore, the results presented here represent a relevant genetic resource for biological studies on evolution, conservation, genetic diversity, population structure and genetic management of breeding stocks of this important species.

Keywords: Patagonian toothfish, NGS, Transcriptome, EST-SSR, genetic diversity

Received: 02 Sep 2019; Accepted: 06 Nov 2019.

Copyright: © 2019 Touma, García, Bravo, Leiva, Moya, Reyes and Vidal. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Rodrigo Vidal, Universidad de Santiago de Chile, Santiago, 9170022, Metropolitan Region, Chile, ruben.vidal@usach.cl