Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms

Hennon, Gwenn M. M.; Dyhrman, Sonya T.

doi:10.1016/j.hal.2019.03.005

Cited by 58 publications

(44 citation statements)

References 178 publications

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“…An alternative approach consists of the generation and application of monoclonal antibodies directed against intracellular antigens of the toxic dinoflagellate Alexandrium minutum as described by Carrera et al (2010) [ 89 ]. Recent proteomic studies have contributed to enlarge the volume of data in sequence databases suitable to identify how the proteomes of HABs are modulated by physiological parameters and in response to changes in the environment, such as climate change [ 90 ]. In that regard, Piñeiro et al (2010) [ 91 ] reviewed the application of proteomics methods to study the effects of climate change on the quality and safety of wild and cultivated seafood products.…”

Section: Application Of Proteomics To Evaluate the Farming Conditimentioning

confidence: 99%

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

Carrera

Piñeiro

Martı́nez

2020

Foods

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This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

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Section: Application Of Proteomics To Evaluate the Farming Conditimentioning

confidence: 99%

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

Carrera

Piñeiro

Martı́nez

2020

Foods

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“…ESTs serve as markers for genes expressed under specific conditions and can be used as probes in the recovery of full-length cDNA or genomic sequences, recognition of exon and intron boundaries, delineation of protein families, and development of probes for genome wide expression profiling [52,63,82,83]. Furthermore, transcriptomic surveys by way of next-generation sequencing (NGS) RNA-Seq, in particular, have illuminated our understanding of the unique biology, metabolism, and ecology of dinoflagellates [82,84,85]. In this review, we summarize our current understanding of the genetic basis of toxin biosynthesis in dinoflagellates and discuss the future directions for this field.…”

Section: Dinoflagellate Genomicsmentioning

confidence: 99%

The Genetic Basis of Toxin Biosynthesis in Dinoflagellates

et al. 2019

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In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.

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“…Gaining better insight into the biology of dinoflagellates is critical to conceive strategies to manage harmful algal blooms, which are projected to become more frequent and severe as a consequence of climate change 7 , and to minimize coral reef loss 4 . Importantly, dinoflagellates seem to defy many of the cellular features found in other eukaryotes.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly of the coral endosymbiontSymbiodinium microadriaticumgenome provides insight into the unique biology of dinoflagellate chromosomes

Nand

Salazar

et al. 2020

Preprint

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AbstractDinoflagellates are major primary producers in the world’s oceans, the cause of harmful algal blooms, and endosymbionts of marine invertebrates. Much remains to be understood about their biology including their peculiar crystalline chromosomes. Here we used Hi-C to order short read-based sub-scaffolds into 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum. Hi-C data show that chromosomes are folded as linear rods within which loci separated by up to several Mb are highly packed. Each chromosome is composed of a series of structural domains separated by boundaries. Genes are enriched towards the ends of chromosomes and are arranged in unidirectional blocks that alternate between top and bottom strands. Strikingly, the boundaries of chromosomal domains are positioned at sites where transcription of two gene blocks converges, indicating a correlation between gene orientation, transcription and chromosome folding. Some chromosomes are enriched for genes involved in specific biological processes (e.g., photosynthesis, and nitrogen-cycling), and functionally related genes tend to co-occur at adjacent sites in the genome. All chromosomes contain several repeated segments that are enriched in mobile elements. The assembly of the S. microadriaticum genome and initial description of its genetic and spatial organization provide a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.

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Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms

Cited by 58 publications

References 178 publications

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

The Genetic Basis of Toxin Biosynthesis in Dinoflagellates

Chromosome-scale assembly of the coral endosymbiontSymbiodinium microadriaticumgenome provides insight into the unique biology of dinoflagellate chromosomes

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