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Animals
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Genomic and Transcriptomic Studies in Aquaculture
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Genomic and Transcriptomic Studies in Aquaculture

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 May 2024) | Viewed by 4062

Special Issue Editor

Dr. Marcia Saraiva

E-Mail Website
Guest Editor
CIIMAR, Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Porto, Portugal
Interests: aquaculture; molecular; transcriptomics; pathogen
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The aquaculture sector is growing worldwide, stimulated by a number of factors including population increases, dietary shifts, ocean and river sustainability, and advances in aquaculture technology. Genomic information provides powerful tools to enhance physiological research, the results of which may be used to enhance aquaculture production efficiency and animal welfare. Transcriptome profiling can be used in aquaculture for the effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress, and toxicology.

This Special Issue aims to publish high-quality multidisciplinary papers related to the latest advances in the fields of genomic and transcriptomic aquaculture.

In this Special Issue of Animals, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Genomic variations in farmed and wild species.
  • Genome editing and other genetic tools and resources.
  • Mechanisms of regulation and evolutionary conservation at genome and transcriptome levels.

I look forward to receiving your contributions.

Dr. Marcia Saraiva
Guest Editor

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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • aquaculture
  • aquatic animals
  • evolution
  • gene expression regulation
  • pathogen–host interactions
  • omics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

15 pages, 3448 KiB  
Article
Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp (Hypophthalmichthys molitrix)
by Xiaohui Li, Chunyan Zhang, Cui Feng, Zewen Zhang, Nannan Feng, Hang Sha, Xiangzhong Luo, Guiwei Zou and Hongwei Liang
Animals 2024, 14(10), 1451; https://doi.org/10.3390/ani14101451 - 13 May 2024
Cited by 4 | Viewed by 1748
Abstract
Bone morphogenetic protein 6 (BMP-6) is a constituent of the TGF-β superfamily, known for its ability to stimulate bone and cartilage formation. The investigation of bmp6’s involvement in the formation of intermuscular bones in fish has garnered significant attention in recent years. [...] Read more.
Bone morphogenetic protein 6 (BMP-6) is a constituent of the TGF-β superfamily, known for its ability to stimulate bone and cartilage formation. The investigation of bmp6’s involvement in the formation of intermuscular bones in fish has garnered significant attention in recent years. The rib cage is an important skeletal structure that plays a protective function for internal organs in fish. However, there has been limited research conducted on the effects of the bmp6 gene on rib development. Silver carp is one of four major fish in China, favoured for its affordability and tender muscle. Nevertheless, the presence of numerous intermuscular bones in silver carp significantly hinders the advancement of its palatability and suitability for processing. This study showcases the effective utilisation of CRISPR/Cas9 technology for the purpose of disrupting the bmp6 gene in silver carp, leading to the creation of chimeras in the P0 generation, marking the first instance of such an achievement. The chimeras exhibited complete viability, normal appearance, and partial intermuscular bones loss, with approximately 30% of them displaying rib bifurcation or bending. Subsequently, a transcriptome analysis on ribs of P0 chimeras and wild-type silver carp was conducted, leading to the identification of 934 genes exhibiting differential expression, of which 483 were found to be up-regulated and 451 were found to be down-regulated. The results of the KEGG analysis revealed that the “NF-kappa B signalling pathway”, “Hippo signalling pathway”, “osteoclast differentiation”, and “haematopoietic cell lineage” exhibited enrichment and displayed a significant correlation with bone development. The up-regulated genes such as tnfα, fos, and ctgf in pathways may facilitate the proliferation and differentiation of osteoclasts, whereas the down-regulation of genes such as tgfb2 and tgfbr1 in pathways may hinder the formation and specialisation of osteoblasts, ultimately resulting in rib abnormalities. This study presents novel findings on the impact of bmp6 gene deletion on the rib development of silver carp, while simultaneously investigating the previously unexplored molecular mechanisms underlying rib defects in fish. Full article
(This article belongs to the Special Issue Genomic and Transcriptomic Studies in Aquaculture)
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27 pages, 6087 KiB  
Article
Whole-Genome Sequencing Analyses Reveal the Evolution Mechanisms of Typical Biological Features of Decapterus maruadsi
by Wen-Jian Deng, Qian-Qian Li, Hao-Nan Shuai, Ren-Xie Wu, Su-Fang Niu, Qing-Hua Wang and Ben-Ben Miao
Animals 2024, 14(8), 1202; https://doi.org/10.3390/ani14081202 - 17 Apr 2024
Viewed by 1804
Abstract
Decapterus maruadsi is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on D. maruadsi [...] Read more.
Decapterus maruadsi is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on D. maruadsi is not comprehensive. Herein, a high-quality chromosome-level genome of a male D. maruadsi was assembled. The assembled genome length was 716.13 Mb with contig N50 of 19.70 Mb. Notably, we successfully anchored 95.73% contig sequences into 23 chromosomes with a total length of 685.54 Mb and a scaffold N50 of 30.77 Mb. A total of 22,716 protein-coding genes, 274.90 Mb repeat sequences, and 10,060 ncRNAs were predicted, among which 22,037 (97%) genes were successfully functionally annotated. The comparative genome analysis identified 459 unique, 73 expanded, and 52 contracted gene families. Moreover, 2804 genes were identified as candidates for positive selection, of which some that were related to the growth and development of bone, muscle, cardioid, and ovaries, such as some members of the TGF-β superfamily, were likely involved in the evolution of typical biological features in D. maruadsi. The study provides an accurate and complete chromosome-level reference genome for further genetic conservation, genomic-assisted breeding, and adaptive evolution research for D. maruadsi. Full article
(This article belongs to the Special Issue Genomic and Transcriptomic Studies in Aquaculture)
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