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Genetics and Genomics of Phytoplankton
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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: closed (29 November 2019) | Viewed by 41562

Special Issue Editors

Prof. Dr. Karin Rengefors

E-Mail Website
Guest Editor
Department of Biology, Lund University, Box 117, Sweden
Interests: phytoplankton; population genetics and genomics; dispersal; speciation
Dr. Gwenael Piganeau

E-Mail Website
Guest Editor
Department of Integrative Biology of Marine Organisms, CNRS, 75016 Paris, France
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 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. 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 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

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

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Published Papers (7 papers)

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13 pages, 1305 KiB  
Article
Genome Resolved Biogeography of Mamiellales
by Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenael Piganeau and Olivier Jaillon
Genes 2020, 11(1), 66; https://doi.org/10.3390/genes11010066 - 7 Jan 2020
Cited by 21 | Viewed by 4848
Abstract
Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven [...] Read more.
Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales’ biogeography and raise novel testable hypotheses about their life cycle and ecology. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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25 pages, 4170 KiB  
Article
Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus
by Aikaterini Pargana, Francesco Musacchia, Remo Sanges, Monia Teresa Russo, Maria Immacolata Ferrante, Chris Bowler and Adriana Zingone
Genes 2020, 11(1), 9; https://doi.org/10.3390/genes11010009 - 20 Dec 2019
Cited by 16 | Viewed by 4091
Abstract
Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the [...] Read more.
Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 °C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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19 pages, 1192 KiB  
Article
Evolution of Codon Usage Bias in Diatoms
by Marc Krasovec and Dmitry A. Filatov
Genes 2019, 10(11), 894; https://doi.org/10.3390/genes10110894 - 6 Nov 2019
Cited by 15 | Viewed by 3822
Abstract
Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection [...] Read more.
Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process—frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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14 pages, 2456 KiB  
Article
Characterization of Aminoacyl-tRNA Synthetases in Chromerids
by Abdoallah Sharaf, Ansgar Gruber, Kateřina Jiroutová and Miroslav Oborník
Genes 2019, 10(8), 582; https://doi.org/10.3390/genes10080582 - 31 Jul 2019
Cited by 7 | Viewed by 5073
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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21 pages, 1631 KiB  
Article
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
by Maria Immacolata Ferrante, Laura Entrambasaguas, Mathias Johansson, Mats Töpel, Anke Kremp, Marina Montresor and Anna Godhe
Genes 2019, 10(7), 494; https://doi.org/10.3390/genes10070494 - 28 Jun 2019
Cited by 20 | Viewed by 6678
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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10 pages, 1429 KiB  
Article
Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes
by Ingrid Sassenhagen and Karin Rengefors
Genes 2019, 10(3), 245; https://doi.org/10.3390/genes10030245 - 22 Mar 2019
Cited by 2 | Viewed by 4585
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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16 pages, 2055 KiB  
Technical Note
Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol
by Frédéric Sanchez, Solène Geffroy, Manon Norest, Sheree Yau, Hervé Moreau and Nigel Grimsley
Genes 2019, 10(5), 399; https://doi.org/10.3390/genes10050399 - 26 May 2019
Cited by 18 | Viewed by 11259
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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