De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics
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-evolu...
Published in: | Frontiers in Marine Science |
---|---|
Main Authors: | , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Frontiers Media S.A.
2019
|
Subjects: | |
Online Access: | https://doi.org/10.3389/fmars.2019.00720 https://doaj.org/article/7e670e5e8eef43f2b6c4a5f853d50421 |
id |
ftdoajarticles:oai:doaj.org/article:7e670e5e8eef43f2b6c4a5f853d50421 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:7e670e5e8eef43f2b6c4a5f853d50421 2023-05-15T13:57:29+02:00 De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics Jorge Touma Killen Ko García Scarleth Bravo Francisco Leiva Javier Moya Luis Vargas-Chacoff Alberto Reyes Rodrigo Vidal 2019-11-01T00:00:00Z https://doi.org/10.3389/fmars.2019.00720 https://doaj.org/article/7e670e5e8eef43f2b6c4a5f853d50421 EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fmars.2019.00720/full https://doaj.org/toc/2296-7745 2296-7745 doi:10.3389/fmars.2019.00720 https://doaj.org/article/7e670e5e8eef43f2b6c4a5f853d50421 Frontiers in Marine Science, Vol 6 (2019) Patagonian toothfish NGS transcriptome EST-SSR genetic diversity Science Q General. Including nature conservation geographical distribution QH1-199.5 article 2019 ftdoajarticles https://doi.org/10.3389/fmars.2019.00720 2022-12-31T12:18:03Z 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 1.12 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 (FST, range 0.082–0.117 and GST′, 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. Article in Journal/Newspaper Antarc* Antarctic Patagonian Toothfish Directory of Open Access Journals: DOAJ Articles Antarctic Pacific Frontiers in Marine Science 6 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Patagonian toothfish NGS transcriptome EST-SSR genetic diversity Science Q General. Including nature conservation geographical distribution QH1-199.5 |
spellingShingle |
Patagonian toothfish NGS transcriptome EST-SSR genetic diversity Science Q General. Including nature conservation geographical distribution QH1-199.5 Jorge Touma Killen Ko García Scarleth Bravo Francisco Leiva Javier Moya Luis Vargas-Chacoff Alberto Reyes Rodrigo Vidal De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
topic_facet |
Patagonian toothfish NGS transcriptome EST-SSR genetic diversity Science Q General. Including nature conservation geographical distribution QH1-199.5 |
description |
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 1.12 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 (FST, range 0.082–0.117 and GST′, 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. |
format |
Article in Journal/Newspaper |
author |
Jorge Touma Killen Ko García Scarleth Bravo Francisco Leiva Javier Moya Luis Vargas-Chacoff Alberto Reyes Rodrigo Vidal |
author_facet |
Jorge Touma Killen Ko García Scarleth Bravo Francisco Leiva Javier Moya Luis Vargas-Chacoff Alberto Reyes Rodrigo Vidal |
author_sort |
Jorge Touma |
title |
De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
title_short |
De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
title_full |
De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
title_fullStr |
De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
title_full_unstemmed |
De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics |
title_sort |
de novo assembly and characterization of patagonian toothfish transcriptome and develop of est-ssr markers for population genetics |
publisher |
Frontiers Media S.A. |
publishDate |
2019 |
url |
https://doi.org/10.3389/fmars.2019.00720 https://doaj.org/article/7e670e5e8eef43f2b6c4a5f853d50421 |
geographic |
Antarctic Pacific |
geographic_facet |
Antarctic Pacific |
genre |
Antarc* Antarctic Patagonian Toothfish |
genre_facet |
Antarc* Antarctic Patagonian Toothfish |
op_source |
Frontiers in Marine Science, Vol 6 (2019) |
op_relation |
https://www.frontiersin.org/article/10.3389/fmars.2019.00720/full https://doaj.org/toc/2296-7745 2296-7745 doi:10.3389/fmars.2019.00720 https://doaj.org/article/7e670e5e8eef43f2b6c4a5f853d50421 |
op_doi |
https://doi.org/10.3389/fmars.2019.00720 |
container_title |
Frontiers in Marine Science |
container_volume |
6 |
_version_ |
1766265154504228864 |