AUTHOR=Touma Jorge , García Killen Ko , Bravo Scarleth , Leiva Francisco , Moya Javier , Vargas-Chacoff Luis , Reyes Alberto , Vidal Rodrigo 

TITLE=De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics

JOURNAL=Frontiers in Marine Science

VOLUME=6

YEAR=2019

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2019.00720

DOI=10.3389/fmars.2019.00720

ISSN=2296-7745

ABSTRACT=<p>Patagonian toothfish (<italic>Dissostichus eleginoides</italic>) 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 <italic>de novo</italic> 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 1.12 kB. 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 25 immune loci were selected for its evaluation as potential EST-SSR population markers. Of this subset, 11 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 (F<sub>ST</sub>, range 0.082–0.117 and <inline-formula><mml:math id="INEQ1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mtext>G</mml:mtext><mml:mrow><mml:mtext>ST</mml:mtext></mml:mrow><mml:mo>′</mml:mo></mml:msubsup></mml:math></inline-formula>, range 0.069–0.291) genetic differentiation (<italic>P</italic> &lt; 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.</p>