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Fishes
Special Issues
Advances in Fish Genome and Transcriptomes
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Advances in Fish Genome and Transcriptomes

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 2393

Special Issue Editor

Prof. Dr. Qiuning Liu

E-Mail Website
Guest Editor
School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
Interests: fish; genomics; immunity; transcriptome; toxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the rapid development of next-generation sequencing technologies and bioinformatics, many high-quality fish genomes have been sequenced. This genomic work provides abundant genetic resources for a deep understanding of divergence, evolution and adaptation in the fish genomes. The transcriptome is a powerful tool that provides a better understanding of the molecular mechanisms underlying adaptation to extreme conditions such as temperature, pH, and more. It also aids in comprehending processes like sex determination, environmental adaptation, defense mechanisms, molecular breeding, nutrition regulation, and more. This tool is particularly beneficial for studying non-sequenced genome fish. I am pleased to invite you to contribute to this Special Issue on “Advances in Fish Genome and Transcriptomes” in the Fishes journal to enhance basic fish research and contribute to efforts aimed at conserving fish biodiversity and promoting the sustainable utilization of natural fish resources.

Prof. Dr. Qiuning Liu
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. Fishes 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

  • fish
  • genomics
  • transcriptomics
  • acclimatization
  • molecular mechanisms
  • adaptive evolution

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

Published Papers (2 papers)

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Research

16 pages, 2324 KiB  
Article
Chromosome-Level Genome Assembly and Comparative Genomic Analysis of the Barbel Chub (Squaliobarbus curriculus) by Integration of PacBio Sequencing and Hi-C Technology
by Baidong Zhang, Yanling Sun, Yang Liu, Xiaojun Song, Su Wang, Tiaoyi Xiao and Pin Nie
Fishes 2024, 9(8), 327; https://doi.org/10.3390/fishes9080327 - 20 Aug 2024
Viewed by 523
Abstract
The barbel chub (Squaliobarbus curriculus), the only species in the genus, is widely distributed in freshwater lakes and rivers at different latitudes in East Asia, with fishery and biodiversity importance, and is an emerging commercially important fish in China. However, the [...] Read more.
The barbel chub (Squaliobarbus curriculus), the only species in the genus, is widely distributed in freshwater lakes and rivers at different latitudes in East Asia, with fishery and biodiversity importance, and is an emerging commercially important fish in China. However, the resource of this species has dramatically declined due to anthropogenic activities such as over-exploitation, as well as water pollution. Genomic resources for S. curriculus are useful for the management and sustainable utilization of this important fish species, and also for a better understanding of its genetic variation in the region. Here, we report the chromosome-level assembly of the S. curriculus genome obtained from the integration of PacBio long sequencing and Hi-C technology. A total of 155.34 Gb high-quality PacBio sequences were generated, and the preliminary genome assembly was 894.95 Mb in size with a contig N50 being 20.34 Mb. By using Hi-C data, 99.42% of the assembled sequences were anchored to 24 pseudochromosomes, with chromosome lengths ranging from 27.22 to 58.75 Mb. A total of 25,779 protein-coding genes were predicted, 94.70% of which were functionally annotated. Moreover, S. curriculus shows resistance to grass carp haemorrhagic disease (GCHD) caused by grass carp reovirus (GCRV), which seriously hinders the status and future perspectives of commercial grass carp production. Phylogenetic analysis indicated that S. curriculus diverged with grass carp (Ctenopharyngodon idellus) approximately 20.80 million years ago. Annotations of the expanded gene families were found to be largely enriched in immune-related KEGG pathway categories. Moreover, a total of 18 Toll-like receptor (TLR) genes were identified from the whole genome of S. curriculus. The high-quality genome assembled in this study will provide a valuable resource for accelerating ecological, evolutionary, and genetic research on S. curriculus. Full article
(This article belongs to the Special Issue Advances in Fish Genome and Transcriptomes)
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15 pages, 3126 KiB  
Article
Transcriptome Analysis Revealed Potential Immune-Related Genes of Head Kidney in the Yellow Catfish (Pelteobagrus fulvidraco) Challenged with Aeromonas hydrophila
by Senhao Jiang, Yuting Lei, Ti Wang, Ruiting Ma, Chunqiang Hou and Qiuning Liu
Fishes 2024, 9(3), 100; https://doi.org/10.3390/fishes9030100 - 6 Mar 2024
Viewed by 1464
Abstract
Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater fish species in aquaculture. However, as intensive farming has rapidly expanded, infectious diseases caused by various bacteria, such as Aeromonas hydrophila, have also increased. We conducted a transcriptomic analysis of head kidney [...] Read more.
Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater fish species in aquaculture. However, as intensive farming has rapidly expanded, infectious diseases caused by various bacteria, such as Aeromonas hydrophila, have also increased. We conducted a transcriptomic analysis of head kidney from P. fulvidraco stimulated by A. hydrophila strain SHOU. A total of 43,249 unigenes with an average length of 1342 bp were obtained following assembly and annotation. By analyzing GO and KEGG enrichment, many differentially expressed genes (DEGs) and pathways related to immunity were identified. Out of the 973 DEGs that were identified, 553 were upregulated and 420 were downregulated. Moreover, KEGG enrichment analysis revealed that the innate immune system, including the TNF signaling pathway, NF-kappa B signaling pathway, and the Toll-like receptor signaling pathway involved in the defense, is activated against infectious response. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis demonstrated that immune response genes were upregulated in response to A. hydrophila stimulation compared to the control. In conclusion, this study provides valuable insights into the immune defense mechanism of P. fulvidraco and sheds light on the host immune genes involved in the response to bacterial infection. Full article
(This article belongs to the Special Issue Advances in Fish Genome and Transcriptomes)
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