Special Issue "Dinoflagellate Biology in the Omics Era"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 May 2019

Special Issue Editors

Guest Editor
Prof. Dr. David Morse

Institut de Recherche en BiologieVégétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke east, Montréal, QC H1X 2B2, Canada
Website | E-Mail
Guest Editor
Prof. Dr. Senjie Lin

Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
Website | E-Mail
Fax: +1 860 405 9153
Interests: marine algae; eukaryotic microbes; molecular ecology; functional genomics; microbial interactions

Special Issue Information

Dear Colleagues,

Dinoflagellates are important players in the marine ecosystem, as they are involved in coral symbiosis, can cause the formation of harmful algal blooms and contribute an important fraction of the ocean’s primary production. Furthermore, dinoflagellates have many unusual cellular features, including chromosomes that remain condensed throughout the cell cycle without histones, chloroplasts that are derived from a secondary endosymbiosis, and an ability to synthesize a wide range of toxins.

For this Special Issue of Microorganisms, we invite you to send contributions concerning any aspect of dinoflagellate biology examined using genomics, transcriptomics, proteomics or metabolomics.

Prof. Dr. David Morse
Prof. Dr. Senjie Lin
Guest Editors

Manuscript Submission Information

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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. Microorganisms 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 1000 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.

Published Papers (3 papers)

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Research

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Open AccessArticle Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii
Microorganisms 2019, 7(4), 96; https://doi.org/10.3390/microorganisms7040096
Received: 26 February 2019 / Revised: 18 March 2019 / Accepted: 30 March 2019 / Published: 2 April 2019
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Abstract
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal [...] Read more.
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses. Full article
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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Review

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Open AccessReview Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes
Microorganisms 2019, 7(2), 27; https://doi.org/10.3390/microorganisms7020027
Received: 21 December 2018 / Revised: 12 January 2019 / Accepted: 17 January 2019 / Published: 22 January 2019
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Abstract
Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations [...] Read more.
Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions. Full article
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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Open AccessReview Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins
Microorganisms 2018, 6(4), 128; https://doi.org/10.3390/microorganisms6040128
Received: 8 November 2018 / Revised: 29 November 2018 / Accepted: 11 December 2018 / Published: 14 December 2018
Cited by 1 | PDF Full-text (1977 KB) | HTML Full-text | XML Full-text
Abstract
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates “dinokaryon” have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed [...] Read more.
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates “dinokaryon” have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented. Full article
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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