Marine Transcriptomic

A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (15 August 2021) | Viewed by 6765

Special Issue Editor


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Guest Editor
Laboratory of Biology of Aquatic Organisms and Ecosystems, Université de Caen Normandie, Caen, France
Interests: transcriptomics; peptidomic; proteomics; immunity; neuropeptides; antimicrobial peptides
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Special Issue Information

Dear Colleagues,

Advances in bioinformatics and the increasing availability of sequenced genomes and transcriptomes provide more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts from marine organisms.

In silico analysis of genomic or transcriptomic data is easier and more efficient today thanks to the development of new bioinformatics tools allowing access to multiple pieces of information and functionalities.

RNA-Sequencing allows detecting both known and novel features, to access differential expressions, gene networks, functions likely to reveal new molecules of interest.

For example, many microorganisms have the potential to produce a far greater number of natural products than have been isolated to date, since most biosynthetic gene clusters are either silent or expressed at very low levels when they are cultured under standard laboratory conditions.

On the other hand, in silico analysis of transcriptomes from other marine organisms such as venomous animals or organisms from extreme environments provides a considerable opportunity to identify new molecules with global health potential.

The identification of biosynthetic gene and gene clusters through a bioinformatics approach and their synthesis by eventual heterologous expression, will give a great impulse for natural products identification and drug discovery from marine organisms.

Dr. Céline Zatylny-Gaudin
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. Marine Drugs 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 2900 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

  • marine organisms
  • bioinformatics
  • biosynthetic gene
  • transcriptomes
  • gene clusters
  • heterologous expression
  • drug discovery
  • in silico analysis

Published Papers (2 papers)

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Research

20 pages, 5018 KiB  
Article
Marine Transcriptomics Analysis for the Identification of New Antimicrobial Peptides
by Baptiste Houyvet, Yolande Bouchon-Navaro, Claude Bouchon, Erwan Corre and Céline Zatylny-Gaudin
Mar. Drugs 2021, 19(9), 490; https://doi.org/10.3390/md19090490 - 28 Aug 2021
Cited by 4 | Viewed by 2828
Abstract
Antimicrobial peptides (AMPs) participate in the immune system to avoid infection, are present in all living organisms and can be used as drugs. Fish express numerous AMP families including defensins, cathelicidins, liver-expressed antimicrobial peptides (LEAPs), histone-derived peptides, and piscidins (a fish-specific AMP family). [...] Read more.
Antimicrobial peptides (AMPs) participate in the immune system to avoid infection, are present in all living organisms and can be used as drugs. Fish express numerous AMP families including defensins, cathelicidins, liver-expressed antimicrobial peptides (LEAPs), histone-derived peptides, and piscidins (a fish-specific AMP family). The present study demonstrates for the first time the occurrence of several AMPs in lionfish (Pterois volitans). Using the lionfish transcriptome, we identified four transcript sequences encoding cysteine-rich AMPs and two new transcripts encoding piscidin-like peptides. These AMPs are described for the first time in a species of the Scorpaenidae family. A functional approach on new pteroicidins was carried out to determine antimicrobial sequences and potential uses, with a view to using some of these AMPs for human health or in aquaculture. Full article
(This article belongs to the Special Issue Marine Transcriptomic)
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29 pages, 6385 KiB  
Article
Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides
by Emilie Réalis-Doyelle, Julie Schwartz, Cédric Cabau, Lorane Le Franc, Benoit Bernay, Guillaume Rivière, Christophe Klopp and Pascal Favrel
Mar. Drugs 2021, 19(8), 452; https://doi.org/10.3390/md19080452 - 7 Aug 2021
Cited by 4 | Viewed by 3439
Abstract
The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Crassostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 [...] Read more.
The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Crassostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms. Full article
(This article belongs to the Special Issue Marine Transcriptomic)
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