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Penaeid Shrimp Genomics and Post-Genomics
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Penaeid Shrimp Genomics and Post-Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 August 2023) | Viewed by 7815

Special Issue Editors

Dr. Fuhua Li

E-Mail Website
Guest Editor
Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
Interests: crustaceans; genomics; functional genomics; immunity; genetics; reproductive biology; genetic breeding
Dr. Acacia Alcivar-Warren

E-Mail Website
Guest Editor
Fundación para la Conservation de la Biodiversidad Acuática y Terrestre (FUCOBI), Quito EC1701, Ecuador
Interests: one Health; shrimp genomics; epigenomics; transposable elements; nimaviruses; endocrine disruptors; transgenerational epigenetic inheritance

Special Issue Information

Dear Colleagues,

Shrimp is the most important internationally traded fishery commodity in terms of value, with a global market valued at USD 37.6 billion in 2021. Despite its economic importance, research on penaeid shrimp genomics and epigenomics is lacking. So far, draft genome assemblies are available for only five penaeid species: P. monodon, P. vannamei, P. japonicus, P. chinensis, and P. indicus. Research is needed to fill the gaps in the genome assemblies in order to address susceptibility to diseases caused by viral and bacterial pathogens, and environmental contamination, and further for application of molecular genetic breeding techniques in shrimp.

In this Special Issue of Genes, we welcome reviews or original articles covering genomic, epigenomic, or post-genomic profiling of penaeid shrimp that may provide the clues to solve the mechanisms of pathogenesis, evolution, and resilience to environmental change. For example, whole exomes, genomes and gene–environment susceptible microbiomes, metabolomes, proteomes, transcriptomes, and methylomes can individually and/or collectively inform specific molecular mechanisms, leading to the potential identification of factors or simple sequence repeats, transposable elements, and epigenetic marks to study transgenerational epigenetic inheritance of disease tolerance. This will eventually identify the most effective genomic selection approaches and precise treatments for emerging diseases.

We look forward to your contribution.

Dr. Fuhua Li
Dr. Acacia Alcivar-Warren
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

 

Keywords

  • penaeid shrimp
  • genomics
  • epigenomics
  • transcriptomes
  • single-cell RNA-seq
  • assembly strategies
  • comparative genomics
  • genomic selection/breeding
  • molecular mechanisms and pathways
  • endogenous viral elements
  • shrimp diseases
  • transgenerational epigenetic inheritance
  • non-coding RNAs

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Published Papers (3 papers)

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Research

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12 pages, 2481 KiB  
Article
The Responses of Alternative Splicing during Heat Stress in the Pacific White Shrimp Litopenaeus vannamei
by Xiaoxi Zhang, Xiaojun Zhang, Jianbo Yuan and Fuhua Li
Genes 2023, 14(7), 1473; https://doi.org/10.3390/genes14071473 - 19 Jul 2023
Cited by 6 | Viewed by 1792
Abstract
Heat tolerance is increasingly becoming a crucial trait for aquaculture species in the face of rapidly changing climate conditions. Alternative splicing (AS) is a vital mechanism within cells that modulates gene abundance and functional diversity, enabling organisms to effectively respond to diverse stressful [...] Read more.
Heat tolerance is increasingly becoming a crucial trait for aquaculture species in the face of rapidly changing climate conditions. Alternative splicing (AS) is a vital mechanism within cells that modulates gene abundance and functional diversity, enabling organisms to effectively respond to diverse stressful conditions, including thermal stress. However, it is still uncertain whether AS contributes to heat tolerance in shrimp. In this study, we conducted an extensive transcriptome analysis on the Pacific white shrimp, Litopenaeus vannamei, revealing a total of 1267, 987, and 130 differential AS events (DAS) in the gill, hepatopancreas, and muscle, respectively, following exposure to heat stress. Among all of the DAS events, exon skipping (ES) was the predominant form of splicing modification observed. Interestingly, a minor portion of DAS genes exhibited overlap across the three tissues, implying that heat stress exerts unique effects on various tissue types. Moreover, the functional enrichment analysis demonstrated that commonly identified DAS genes were primarily associated with the “spliceosome” pathway, indicating that the AS of splicing-related genes played a crucial role in the response to heat stress. Our findings also revealed that heat stress tended to induce longer mRNA isoforms through differential alternative 3′ splice site (A3SS) events. Notably, A3SS events exhibited the highest proportion of maintained open reading frames (ORFs) under heat stress. Interestingly, we observed a limited overlap between the genes exhibiting DAS and those showing differential gene expression (DEG), indicating that AS may function as a distinct regulatory mechanism independent of transcriptional regulation in response to heat stress. This is the first comprehensive study on AS in crustacea species under heat stress, which broadens our understanding of the regulatory mechanisms governing the crustaceans’ response to environmental stress, providing valuable insights for the aquaculture breeding of shrimp and other aquatic animals. Full article
(This article belongs to the Special Issue Penaeid Shrimp Genomics and Post-Genomics)
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Review

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21 pages, 362 KiB  
Review
Genomics of Shrimp Allergens and Beyond
by Shanshan Li, Ka Hou Chu and Christine Yee Yan Wai
Genes 2023, 14(12), 2145; https://doi.org/10.3390/genes14122145 - 27 Nov 2023
Cited by 6 | Viewed by 1762
Abstract
Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the “Big Eight” allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the [...] Read more.
Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the “Big Eight” allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the most consumed crustaceans triggering immunoglobulin E (IgE)-mediated allergic reactions. Over the past decades, the allergen repertoire of shrimp has been unveiled based on conventional immunodetection methods. With the availability of genomic data for penaeid shrimp and other technological advancements like transcriptomic approaches, new shrimp allergens have been identified and directed new insights into their expression levels, cross-reactivity, and functional impact. In this review paper, we summarize the current knowledge on shrimp allergens, as well as allergens from other crustaceans and mollusks. Specific emphasis is put on the genomic information of the shrimp allergens, their protein characteristics, and cross-reactivity among shrimp and other organisms. Full article
(This article belongs to the Special Issue Penaeid Shrimp Genomics and Post-Genomics)
26 pages, 2203 KiB  
Review
Epigenetic Modulations for Prevention of Infectious Diseases in Shrimp Aquaculture
by Gunasekara Chathura Wikumpriya, Madhuranga Walawedurage Srinith Prabhatha, Jiye Lee and Chan-Hee Kim
Genes 2023, 14(9), 1682; https://doi.org/10.3390/genes14091682 - 25 Aug 2023
Cited by 4 | Viewed by 3498
Abstract
Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, in particular, holds a significant role in the global economy and food security, providing a rich source of nutrients for human consumption. Nonetheless, the industry faces formidable challenges, [...] Read more.
Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, in particular, holds a significant role in the global economy and food security, providing a rich source of nutrients for human consumption. Nonetheless, the industry faces formidable challenges, primarily attributed to disease outbreaks and the diminishing efficacy of conventional disease management approaches, such as antibiotic usage. Consequently, there is an urgent imperative to explore alternative strategies to ensure the sustainability of the industry. In this context, the field of epigenetics emerges as a promising avenue for combating infectious diseases in shrimp aquaculture. Epigenetic modulations entail chemical alterations in DNA and proteins, orchestrating gene expression patterns without modifying the underlying DNA sequence through DNA methylation, histone modifications, and non-coding RNA molecules. Utilizing epigenetic mechanisms presents an opportunity to enhance immune gene expression and bolster disease resistance in shrimp, thereby contributing to disease management strategies and optimizing shrimp health and productivity. Additionally, the concept of epigenetic inheritability in marine animals holds immense potential for the future of the shrimp farming industry. To this end, this comprehensive review thoroughly explores the dynamics of epigenetic modulations in shrimp aquaculture, with a particular emphasis on its pivotal role in disease management. It conveys the significance of harnessing advantageous epigenetic changes to ensure the long-term viability of shrimp farming while deliberating on the potential consequences of these interventions. Overall, this appraisal highlights the promising trajectory of epigenetic applications, propelling the field toward strengthening sustainability in shrimp aquaculture. Full article
(This article belongs to the Special Issue Penaeid Shrimp Genomics and Post-Genomics)
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