Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review

Tan, Min Pau; Wong, Li Lian; Razali, Siti Aisyah; Afiqah‐Aleng, Nor; Nor, Siti Azizah Mohd; Sung, Yeong Yik; Peer, Yves Van de; Sorgeloos, Patrick; Danish-Daniel, Muhd

doi:10.1177/1176934319892284

Cited by 21 publications

(17 citation statements)

References 57 publications

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“…Pathogenic and spoilage microorganisms can be introduced into fish and fish products at any point throughout the production and supply chain. The application of next‐generation sequencing (NGS) technologies has allowed in‐depth insights into the fish microbiome—the consortium of all microbial habitants in fish and the surrounding environment—which facilitates better understanding of the sources of pathogenic and spoilage microorganisms (Brugman et al., 2018; Legrand, Wynne, Weyrich, & Oxley, 2019; Marchesi & Ravel, 2015; Ross, Hoffmann, & Neufeld, 2019; Tan et al., 2019; Yukgehnaish et al., 2020). Understanding the prevalence, ecology, concentration, and dynamics of pathogenic and spoilage microorganisms present throughout the entire fish production chain will also contribute to the development and application of new intervention strategies.…”

Section: Introductionmentioning

confidence: 99%

The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies

Sheng

Wang

2020

Comp Rev Food Sci Food Safe

137

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Microorganisms play a crucial and unique role in fish and fish product safety. The presence of human pathogens and the formation of histamine caused by spoilage bacteria make the control of both pathogenic and spoilage microorganisms critical for fish product safety. To provide a comprehensive and updated overview of the involvement of microorganisms in fish and fish product safety, this paper reviewed outbreak and recall surveillance data obtained from government agencies from 1998 to 2018 and identified major safety concerns associated with both domestic and imported fish products. The review also summarized all available literature about the prevalence of major and emerging microbial safety concerns, including Salmonella spp., Listeria monocytogenes, and Aeromonas hydrophila, in different fish and fish products and the survival of these pathogens under different storage conditions. The prevalence of antibiotic‐resistant bacteria (ARB) and antibiotic‐resistant genes (ARGs), two emerging food safety concerns, is also reviewed. Pathogenic and spoilage microorganisms as well as ARB and ARGs can be introduced into fish and fish products in both preharvest and postharvest stages. Many novel intervention strategies have been proposed and tested for the control of different microorganisms on fish and fish products. One key question that needs to be considered when developing and implementing novel control measures is how to ensure that the measures are cost and environment friendly as well as sustainable. Over the years, regulations have been established to provide guidance documents for good farming and processing practices. To be more prepared for the globalization of the food chain, harmonization of regulations is still needed.

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Section: Introductionmentioning

confidence: 99%

The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies

Sheng

Wang

2020

Comp Rev Food Sci Food Safe

137

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“…For example, understanding viral quasispecies variations would allow for the identification of infectious disease routes and transmission in aquatic organisms. 20 Additionally, the complete genome of the white spot syndrome virus (WSSV) was assembled from shrimp tissues via NGS. The WSSV genome was 305,094 bp, from which 38 single nucleotide polymorphisms (SNPs) were detected.…”

Section: Next-generation Sequencing Applications In Viral Disease Resmentioning

confidence: 99%

Coupling cell culture and next-generation sequencing to study aquaculture viral diseases: a review

Mena¹

2021

JAMB

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In this short review, we highlight the importance of combining cell culture and nextgeneration sequencing for the study of viruses in aquaculture. Moreover, we summarize some key examples of previously published studies that have implemented this approach and discuss the advantages of nanopore sequencing and other long-read sequencing technologies. With the rapid advances of genomic research, selection of the best tool to carry out analyses, it's a computational challenge, but the potential for their applications is enormous. Therefore, this mini-review highlights important NGS bioinformatic tools and recent studies in cell culture for the study of aquatic virology.

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“…Các nhà khoa học về sinh vật hoang dã đã kết hợp các nghiên cứu về sinh thái, tiến hóa và hệ gen học để khai thác các dữ liệu lớn về hệ gen, phục vụ nghiên cứu phát sinh chủng loại, phân tích mối quan hệ giữa vật chủ và mầm bệnh, phát hiện các con đường lây nhiễm, phát triển thuốc phòng trị bệnh, bảo tồn các hệ sinh thái (Tan et al, 2019). Sự bùng phát dịch và sự lây nhiễm các mầm bệnh có thể dẫn đến sự suy giảm nghiêm trọng của hệ sinh thái.…”

Section: Trong Lĩnh Vực Môi Trườngunclassified

Genomics and big data: Research, development and applications

Hiền¹,

Văn²,

Oanh³

et al. 2021

Vietnam J. Biotechnol.

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Recent years, genomics and big data analytics have been widely applied and have significant impacts in various important areas of social life worldwide. The development of the next-generation sequencing (NGS) technologies, such as whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome, and/or targeted sequencing, has enabled quickly generating the genomes of interested living organisms. Around the world many nations have invested in and promoted the development of genomics and big data analytics. A number of well-established projects on sequencing of human, animal, plant, and microorganism genomes to generate vast amounts of genomic data have been conducted independently or as collaborative efforts by national or international research networks of scientists specializing in different technical fields of genomics, bioinformatics, computational and statistical biology, automation, artificial intelligence, etc. Complicated and large genomic datasets have been effectively established, storage, managed, and used. Vietnam supports this new field of study through setting up governmental authorized institutions and conducting genomic research projects of human and other endemic organisms. In this paper, the research, development, and applications of genomic big data are reviewed with focusing on: (i) Available sequencing technologies for generating genomic datasets; (ii) Genomics and big data initiatives worldwide; (iii) Genomics and big data analytics in selected countries and Vietnam; (iv) Genomic data applications in key areas including medicine for human health care, agriculture - forestry, food safety, and environment.

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Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review

Cited by 21 publications

References 57 publications

The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies

The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies

Coupling cell culture and next-generation sequencing to study aquaculture viral diseases: a review

Genomics and big data: Research, development and applications

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