Special Issue "Genetics and Genomics of Phytoplankton"

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

Deadline for manuscript submissions: 30 September 2019.

Special Issue Editors

Guest Editor
Prof. Dr. Karin Rengefors

Department of Biology, Lund University, Sweden
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Interests: phytoplankton; population genetics and genomics; dispersal; speciation
Guest Editor
Dr. Gwenael Piganeau

Department of Integrative Biology of Marine Organisms, CNRS, France
E-Mail
Interests: phytoplankton; evolutionary and population genomics; experimental evolution

Special Issue Information

Dear Colleagues

Phytoplankton in marine and freshwater systems around the world play a pivotal role as primary producers in aquatic food webs, in the cycling of nutrients and carbon, and in oxygen production. However, some can also form harmful algal blooms which cause large economic losses, management issues, and serious health effects. Although their ecological importance is largely recognized, much is unknown in terms of the genomic basis of their biology and evolution. One reason is that phytoplankton are extremely diverse, and include members from all the major eukaryotic groups as well as cyanobacteria. With the new sequencing and gene editing methods, it is now possible to address many evolutionary and ecological questions in these non-model organisms.

We are calling for articles for a Special Issue on “Genetics and Genomics of Phytoplankton”, including both eukaryotic and cyanobacterial phytoplankton. We invite both articles looking towards the future (i.e., original articles including short communications), as well as those presenting the state-of-the-art in the form of review papers. We encourage topics focusing on evolutionary genetics and genomics as well as population genetics and genomics, including novel methods papers to address these topics from genome or transcriptome perspectives.

We will accept manuscripts starting February 1st 2019 until the deadline 30 September 2019. Manuscripts will be processed continuously during this period following standard journal procedures. For questions regarding potential paper suitability, please contact the Guest Editors.

Prof. Dr. Karin Rengefors
Dr. Gwenael Piganeau
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 papers will be 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 1800 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

  • genomics
  • transcriptomics
  • functional genomics
  • gene function
  • population genomics
  • evolutionary genetics

Published Papers (4 papers)

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Research

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Open AccessArticle
Characterization of Aminoacyl-tRNA Synthetases in Chromerids
Received: 1 July 2019 / Revised: 23 July 2019 / Accepted: 28 July 2019 / Published: 31 July 2019
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Abstract
Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the [...] Read more.
Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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Open AccessArticle
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
Received: 6 May 2019 / Revised: 14 June 2019 / Accepted: 24 June 2019 / Published: 28 June 2019
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Abstract
Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim [...] Read more.
Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual phase of the centric planktonic diatom Skeletonema marinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschia multistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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Open AccessArticle
Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes
Received: 8 February 2019 / Revised: 19 March 2019 / Accepted: 20 March 2019 / Published: 22 March 2019
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Abstract
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, [...] Read more.
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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Other

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Open AccessTechnical Note
Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol
Received: 15 March 2019 / Revised: 16 May 2019 / Accepted: 21 May 2019 / Published: 26 May 2019
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Abstract
Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced [...] Read more.
Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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