Aquaculture omics: An update on the current status of research and data analysis

Sundaray, Jitendra Kumar; Dixit, Sangita; Rather, Ashraf; Rasal, Kiran D.; Sahoo, Lakshman

doi:10.1016/j.margen.2022.100967

Cited by 12 publications

(4 citation statements)

References 137 publications

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“…The use of applications and websites that allow for the analysis of unique omics data has been widely described, such as the NCBI database, LIPIDSMAPS, Ingenuity Pathway Analysis, Cytoscape, etc. [201,202]. However, researchers have stated that analyzing singletype data is insufficient to understand biological systems, as many levels are used to regulate a system [203].…”

Section: Omics Data and Informatics Toolsmentioning

confidence: 99%

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Machuca-Sepúlveda

Miranda

Lefin

et al. 2023

Biology

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Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.

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Section: Omics Data and Informatics Toolsmentioning

confidence: 99%

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Machuca-Sepúlveda

Miranda

Lefin

et al. 2023

Biology

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“…There have been many review papers concerning the application of molecular markers to aquaculture and the management of fisheries’ resource conservation [ 6 , 7 , 13 , 19 , 20 , 21 , 22 , 23 ]. This review is an attempt to show the benefits of the application of SNPs to recognize natural populations of aquatic animals and to detect threats to them from accidentally or intentionally released farm animals ( Figure 1 ).…”

Section: Introductionmentioning

confidence: 99%

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Wenne

2023

Animals

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An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.

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“…There is another method to analyse the transcriptomic data, which is RNA-seq technology. RNA-seq technology is beneficial in understanding gene expression, gene regulatory networks, metabolic pathways, and protein-protein interaction [5]. Thus, this enables various biological processes to be revealed, such as immune responses and development, stress responses, etc.…”

Section: Introductionmentioning

confidence: 99%

MicroRNA Regulation in Infectious Diseases and Its Potential as a Biosensor in Future Aquaculture Industry: A Review

SiouNing,

Seong,

Kondo

et al. 2023

Molecules

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An infectious disease is the most apprehensive problem in aquaculture as it can lead to high mortality in aquatic organisms and massive economic loss. Even though significant progress has been accomplished in therapeutic, prevention, and diagnostic using several potential technologies, more robust inventions and breakthroughs should be achieved to control the spread of infectious diseases. MicroRNA (miRNA) is an endogenous small non-coding RNA that post-transcriptionally regulates the protein-coding genes. It involves various biological regulatory mechanisms in organisms such as cell differentiation, proliferation, immune responses, development, apoptosis, and others. Furthermore, an miRNA also acts as a mediator to either regulate host responses or enhance the replication of diseases during infection. Therefore, the emergence of miRNAs could be potential candidates for the establishment of diagnostic tools for numerous infectious diseases. Interestingly, studies have revealed that miRNAs can be used as biomarkers and biosensors to detect diseases, and can also be used to design vaccines to attenuate pathogens. This review provides an overview of miRNA biogenesis and specifically focuses on its regulation during infection in aquatic organisms, especially on the host immune responses and how miRNAs enhance the replication of pathogens in the organism. In addition to that, we explored the potential applications, including diagnostic methods and treatments, that can be employed in the aquaculture industry.

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Aquaculture omics: An update on the current status of research and data analysis

Cited by 12 publications

References 137 publications

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

MicroRNA Regulation in Infectious Diseases and Its Potential as a Biosensor in Future Aquaculture Industry: A Review

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