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Yılmaz E, Mann DG, Gastineau R, Trobajo R, Solak CN, Górecka E, Turmel M, Lemieux C, Ertorun N, Witkowski A. Description of Naviculavanseea sp. nov. (Naviculales, Naviculaceae), a new species of diatom from the highly alkaline Lake Van (Republic of Türkiye) with complete characterisation of its organellar genomes and multigene phylogeny. PHYTOKEYS 2024; 241:27-48. [PMID: 38628637 PMCID: PMC11019260 DOI: 10.3897/phytokeys.241.118903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 04/19/2024]
Abstract
The current article describes Naviculavanseeasp. nov., a new species of diatom from Lake Van, a highly alkaline lake in Eastern Anatolia (Türkiye). The description is based on light and scanning electron microscopy performed on two monoclonal cultures. The complete nuclear rRNA clusters and plastid genomes have been sequenced for these two strains and the complete mitogenome for one of them. The plastome of both strains shows the probable loss of a functional ycf35 gene. They also exhibit two IB4 group I introns in their rrl, each encoding for a putative LAGLIDADG homing endonuclease, with the first L1917 IB4 intron reported amongst diatoms. The Maximum Likelihood phylogeny inferred from a concatenated alignment of 18S, rbcL and psbC distinguishes N.vanseea sp. nov. from the morphologically similar species Naviculacincta and Naviculamicrodigitoradiata.
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Affiliation(s)
- Elif Yılmaz
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - David G. Mann
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Rosa Trobajo
- Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 La Ràpita, Catalunya, Spain
| | - Cüneyt Nadir Solak
- Department of Biology, Faculty of Science & Art, Dumlupınar University, 43000 Kütahya, Türkiye
| | - Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Nesil Ertorun
- Department of Biology, Science Faculty, Eskişehir Technical University, 26000 Eskişehir, Türkiye
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
- Deceased
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Seveno J, Car A, Sirjacobs D, Fullgrabe L, Dupčić Radić I, Lejeune P, Leignel V, Mouget JL. Benthic Diatom Blooms of Blue Haslea spp. in the Mediterranean Sea. Mar Drugs 2023; 21:583. [PMID: 37999407 PMCID: PMC10672038 DOI: 10.3390/md21110583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Blue Haslea species are marine benthic pennate diatoms able to synthesize a blue-green water-soluble pigment, like marennine produced by H. ostrearia Simonsen. New species of Haslea synthetizing blue pigments were recently described (H. karadagensis, H. nusantara, H. provincialis and H. silbo). Their marennine-like pigments have allelopathic, antioxidative, antiviral and antibacterial properties, which have been demonstrated in laboratory conditions. Marennine is also responsible for the greening of oysters, for example, in the Marennes Oléron area (France), a phenomenon that has economical and patrimonial values. While blue Haslea spp. blooms have been episodically observed in natural environments (e.g., France, Croatia, USA), their dynamics have only been investigated in oyster ponds. This work is the first description of blue Haslea spp. benthic blooms that develop in open environments on the periphyton, covering turf and some macroalgae-like Padina. Different sites were monitored in the Mediterranean Sea (Corsica, France and Croatia) and two different blue Haslea species involved in these blooms were identified: H. ostrearia and H. provincialis. A non-blue Haslea species was also occasionally encountered. The benthic blooms of blue Haslea followed the phytoplankton spring bloom and occurred in shallow calm waters, possibly indicating a prominent role of light to initiate the blooms. In the absence of very strong winds and water currents that can possibly disaggregate the blue biofilm, the end of blooms coincided with the warming of the upper water masses, which might be profitable for other microorganisms and ultimately lead to a shift in the biofilm community.
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Affiliation(s)
- Julie Seveno
- BIOSSE Laboratory, Le Mans University, 72000 Le Mans, France
- Station de Recherches Sous-Marines et Océanographiques STARESO, 20260 Calvi, France (P.L.)
| | - Ana Car
- Institute for Marine and Coastal Research, University of Dubrovnik, Kneza Damjana Jude 12, 20000 Dubrovnik, Croatia; (A.C.)
| | - Damien Sirjacobs
- InBioS–PhytoSYSTEMS Laboratory, University of Liège, B-4000 Liège, Belgium
| | - Lovina Fullgrabe
- Station de Recherches Sous-Marines et Océanographiques STARESO, 20260 Calvi, France (P.L.)
| | - Iris Dupčić Radić
- Institute for Marine and Coastal Research, University of Dubrovnik, Kneza Damjana Jude 12, 20000 Dubrovnik, Croatia; (A.C.)
| | - Pierre Lejeune
- Station de Recherches Sous-Marines et Océanographiques STARESO, 20260 Calvi, France (P.L.)
| | - Vincent Leignel
- BIOSSE Laboratory, Le Mans University, 72000 Le Mans, France
| | - Jean-Luc Mouget
- BIOSSE Laboratory, Le Mans University, 72000 Le Mans, France
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Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
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Affiliation(s)
- Yichao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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Kim JI, Jo BY, Park MG, Yoo YD, Shin W, Archibald JM. Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:896138. [PMID: 35769291 PMCID: PMC9235467 DOI: 10.3389/fpls.2022.896138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Bok Yeon Jo
- Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
| | - Yeong Du Yoo
- Department of Marine Biology, College of Ocean Sciences and Technology, Kunsan National University, Kunsan, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Gabed N, Verret F, Peticca A, Kryvoruchko I, Gastineau R, Bosson O, Séveno J, Davidovich O, Davidovich N, Witkowski A, Kristoffersen JB, Benali A, Ioannou E, Koutsaviti A, Roussis V, Gâteau H, Phimmaha S, Leignel V, Badawi M, Khiar F, Francezon N, Fodil M, Pasetto P, Mouget JL. What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age. Mar Drugs 2022; 20:md20040234. [PMID: 35447907 PMCID: PMC9033121 DOI: 10.3390/md20040234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).
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Affiliation(s)
- Noujoud Gabed
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Oran High School of Biological Sciences (ESSBO), Cellular and Molecular Biology Department, Oran 31000, Algeria
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
| | - Frédéric Verret
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Correspondence: ; Tel.: +30-2810-337-852
| | - Aurélie Peticca
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Igor Kryvoruchko
- Department of Biology, United Arab Emirates University (UAEU), Al Ain P.O. Box 15551, United Arab Emirates;
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Orlane Bosson
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Julie Séveno
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Olga Davidovich
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Nikolai Davidovich
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Jon Bent Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
| | - Amel Benali
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de la Technologie d’Oran Mohamed BOUDIAF-USTO-MB, BP 1505, El M’naouer, Oran 31000, Algeria
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Aikaterini Koutsaviti
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Vassilios Roussis
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Hélène Gâteau
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Suliya Phimmaha
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Vincent Leignel
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Myriam Badawi
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Feriel Khiar
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Nellie Francezon
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Mostefa Fodil
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Pamela Pasetto
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Jean-Luc Mouget
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
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6
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Solak CN, Gastineau R, Lemieux C, Turmel M, Gorecka E, Trobajo R, Rybak M, Yılmaz E, Witkowski A. Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey). PeerJ 2021; 9:e12220. [PMID: 34733585 PMCID: PMC8544256 DOI: 10.7717/peerj.12220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.
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Affiliation(s)
- Cüneyt Nadir Solak
- Department of Biology, Arts and Science Faculty, Dumlupınar University, Kütahya, Turkey
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Ewa Gorecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Rosa Trobajo
- Marine and Continental Waters Program, IRTA-Institute of Agriculture and Food Research and Technology, Sant Carles de la Ràpita, Catalonia, Spain
| | - Mateusz Rybak
- Department of Agroecology and Forest Utilization, Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Rzeszów, Poland
| | - Elif Yılmaz
- Department of Biology, Arts and Science Faculty, Dumlupınar University, Kütahya, Turkey.,Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
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7
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Górecka E, Gastineau R, Davidovich NA, Davidovich OI, Ashworth MP, Sabir JSM, Lemieux C, Turmel M, Witkowski A. Mitochondrial and Plastid Genomes of the Monoraphid Diatom Schizostauron trachyderma. Int J Mol Sci 2021; 22:ijms222011139. [PMID: 34681800 PMCID: PMC8541233 DOI: 10.3390/ijms222011139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
We provide for the first time the complete plastid and mitochondrial genomes of a monoraphid diatom: Schizostauron trachyderma. The mitogenome is 41,957 bp in size and displays two group II introns in the cox1 gene. The 187,029 bp plastid genome features the typical quadripartite architecture of diatom genomes. It contains a group II intron in the petB gene that overlaps the large single-copy and the inverted repeat region. There is also a group IB4 intron encoding a putative LAGLIDADG homing endonuclease in the rnl gene. The multigene phylogenies conducted provide more evidence of the proximity between S. trachyderma and fistula-bearing species of biraphid diatoms.
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Affiliation(s)
- Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
- Correspondence: (E.G.); (R.G.)
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
- Correspondence: (E.G.); (R.G.)
| | - Nikolai A. Davidovich
- Karadag Scientific Station—Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia; (N.A.D.); (O.I.D.)
| | - Olga I. Davidovich
- Karadag Scientific Station—Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia; (N.A.D.); (O.I.D.)
| | - Matt P. Ashworth
- Department of Molecular Biosciences, NHB, University of Texas at Austin, Austin, TX 78712, USA;
| | - Jamal S. M. Sabir
- Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Claude Lemieux
- Département de Biochimie, Microbiologie et Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Monique Turmel
- Département de Biochimie, Microbiologie et Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
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Gastineau R, Davidovich NA, Davidovich OI, Lemieux C, Turmel M, Wróbel RJ, Witkowski A. Extreme Enlargement of the Inverted Repeat Region in the Plastid Genomes of Diatoms from the Genus Climaconeis. Int J Mol Sci 2021; 22:7155. [PMID: 34281209 PMCID: PMC8268801 DOI: 10.3390/ijms22137155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
We sequenced the plastid genomes of three diatoms from the genus Climaconeis, including two strains formerly designated as Climaconeis scalaris. At 208,097 and 216,580 bp, the plastid genomes of the latter strains are the largest ever sequenced among diatoms and their increased size is explained by the massive expansion of the inverted repeat region. Important rearrangements of gene order were identified among the two populations of Climaconeis cf. scalaris. The other sequenced Climaconeis chloroplast genome is 1.5 times smaller compared with those of the Climaconeis cf. scalaris strains and it features an usual quadripartite structure. The extensive structural changes reported here for the genus Climaconeis are compared with those previously observed for other algae and plants displaying large plastid genomes.
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Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland; (N.A.D.); (A.W.)
| | - Nikolaï A. Davidovich
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland; (N.A.D.); (A.W.)
- Karadag Scientific Station–Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia;
| | - Olga I. Davidovich
- Karadag Scientific Station–Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia;
| | - Claude Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Monique Turmel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Rafał J. Wróbel
- Engineering of Catalytic and Sorbent Materials Department, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology Szczecin, Pułaskiego 10, 70-322 Szczecin, Poland;
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland; (N.A.D.); (A.W.)
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