De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics
| Autor: | Scarleth Bravo, Richard Vidal, Jorge Touma, Francisco Leiva, Alberto Reyes, Javier Moya, Killen Ko Garcia, Luis Vargas-Chacoff |
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| Rok vydání: | 2019 |
| Předmět: |
Dissostichus
lcsh:QH1-199.5 Population Population genetics Sequence assembly Ocean Engineering Locus (genetics) lcsh:General. Including nature conservation geographical distribution Aquatic Science Oceanography Transcriptome EST-SSR Allele lcsh:Science education Water Science and Technology Global and Planetary Change education.field_of_study Genetic diversity biology food and beverages genetic diversity biology.organism_classification Evolutionary biology NGS lcsh:Q Patagonian toothfish transcriptome |
| Zdroj: | Frontiers in Marine Science, Vol 6 (2019) |
| ISSN: | 2296-7745 |
| DOI: | 10.3389/fmars.2019.00720 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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