Genomic Approaches in Marine Biodiversity and Aquaculture

Huete-Pérez, Jorge A.; Quezada, Fernando

doi:10.4067/s0716-97602013000400007

Cited by 23 publications

(12 citation statements)

References 62 publications

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“…The constant interaction of metazoans with the dynamic environmental implicates the presence of several behavioral and physiological phenotypes (Kültz et al, 2013), which are developed in a short period and dependent on genetic variants among populations. Therefore, a clear conclusion suggested by several authors is that both approaches, population genetics and transcriptomic, will be very successful in the area of conservation of natural resources (Huete-Pérez and Quezada, 2013;He et al, 2016;Connon et al, 2018;Filho, 2018). In this context, an evident reason for the limitation of population genetics and functional transcriptome studies in Patagonian toothfish is the scarce number of genetic resources developed for this species (Garcia et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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

Touma

Garcia²,

Bravo³

et al. 2019

Front. Mar. Sci.

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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 (F ST , 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.

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Section: Introductionmentioning

confidence: 99%

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

Touma

Garcia²,

Bravo³

et al. 2019

Front. Mar. Sci.

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“…Biodiversity [7] Disease diagnostics [8] Nutrition [9] Environment [10] Aging disease [11] Forensic biology [12] Agriculture Table 1. The application of NGS in biotechnology.…”

Section: Application Referencesmentioning

confidence: 99%

Explore the Novel Biomarkers through Next-Generation Sequencing

2018

Genotyping

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Next-generation sequencing is being a robust technology for the practice of clinical diagnosis. The reason is that this technology offers the advantage of higher sensitivity and the potential to detect the full genome sequence of pathogens, including unknown pathogen species. In view of the exceptional advantages of next-generation sequencing, the technology can be used to improve and revolutionize conventional pathogenic detection methodologies. The technological result holds great possibilities in helping to support clinicians with richer insights into host's genomic features, including the appropriateness to drug resistance based on the sequencing mapping of the microorganism. Besides, the technology will help discover the source of infection and insights into treatment directions, furthermore lead to the advancements in diagnosis. Eventually, this technology will benefit the clinical community in infectious disease prediction and prevention.

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“…Indeed, there are comprehensive reviews for genomics (Quinn et al . ; Huete‐Pérez & Quezada ), transcriptomics (Saroglia & Liu ; Qian et al . ) and proteomics (Rodrigues et al .…”

Section: Scopementioning

confidence: 99%

Showcasing metabolomic applications in aquaculture: a review

Young

Alfaro

2016

Reviews in Aquaculture

124

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Aquaculture production is currently challenged to meet the growing demands for seafood protein throughout the world. To achieve this growth in an efficient, safe and sustainable manner, novel tools and applications will need to be incorporated at each step of the production line. A variety of 'omics' (e.g., transcriptomics, proteomics, metabolomics) applications have already begun to emerge in aquaculture research with extreme success. A promising new 'omics' approach is metabolomics, which aims to use metabolite profiles to identify biomarkers indicative of physiological responses of living samples (e.g., whole organism, tissues, cells) to environmental or culture conditions. One of the benefits of this approach is that it uses a broad scan of biological conditions to identify often unexpected problem or risk areas to focus management attention. In this contribution, we have selected relevant research examples to showcase the applications of metabolomics in aquaculture in four major areas: hatchery production, nutrition and diet, disease and immunology, and food safety and quality. The novelty of this approach is highlighted by the fact that we have cited the majority of published papers in this field, and these are all recent (within the last decade) contributions.

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Genomic Approaches in Marine Biodiversity and Aquaculture

Cited by 23 publications

References 62 publications

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

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

Explore the Novel Biomarkers through Next-Generation Sequencing

Showcasing metabolomic applications in aquaculture: a review

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