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First Record of Marine Phytoplankton, Picochlorum Maculatum in the Southeastern Coast of India
Indian Journal of Geo Marine Sciences Vol. 46 (04), April 2017, pp. 791-796 First record of marine phytoplankton, Picochlorum maculatum in the Southeastern coast of India Dinesh Kumar, S1. S. Ananth1, P. Santhanam1*, K. Kaleshkumar2 & R. Rajaram2 1Marine Planktonology & Aquaculture Lab., 2DNA Barcoding and Marine Genomics Lab., Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli- 620 024, Tamil Nadu, India. * [E-mail: [email protected], [email protected]] Received 20 October 2014 ; revised 02 January 2015 The marine phytoplankton Picochlorum maculatum (Chlorophyta:Trebouxiophyceae) is recorded for the first time in the Southeastern coast of India. In this study, marine phytoplankton were collected at Muthukkuda mangrove waters, Tamil Nadu, Southeast coast of India which was then isolated, purified and identified with rDNA sequencing. Recurrence component analysis of marine phytoplankton P. maculatum indicated that the peptides were composed of Beta structure, comprising alpha-helix, extended strand and random coil. The number of amino acids and chemical properties from the marine microalgae P. maculatum are calculated and having composition of Neutral (82.69%), Acidic (10.72%) and Basic (6.57%) amino acids. This species may be introduced by way of shipping and other transport mechanisms where organisms are inadvertently moved out of their home range, e.g., ballast water exchange. [Keywords: Microalgae, Picochlorum maculatum, Genetic Distance, Open Reading Frame, Poly A signals] Introduction The genus Picochlorum maculatum was in Indian coastal waters. There are five Picochlorum established by Henley et. al.1 based on Nannochloris were reported in species level from Japan maculta Butcher, 1952. The currently accepted name (Picochlorum atomus, Picochlorum eukaryotum, P. -
Perspectives in Phycology Vol
Perspectives in Phycology Vol. 3 (2016), Issue 3, p. 141–154 Article Published online June 2016 Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences Margot Tragin1, Adriana Lopes dos Santos1, Richard Christen2,3 and Daniel Vaulot1* 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France 2 CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France 3 Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France * Corresponding author: [email protected] With 5 figures in the text and an electronic supplement Abstract: Green algae (Chlorophyta) are an important group of microalgae whose diversity and ecological importance in marine systems has been little studied. In this review, we first present an overview of Chlorophyta taxonomy and detail the most important groups from the marine environment. Then, using public 18S rRNA Chlorophyta sequences from culture and natural samples retrieved from the annotated Protist Ribosomal Reference (PR²) database, we illustrate the distribution of different green algal lineages in the oceans. The largest group of sequences belongs to the class Mamiellophyceae and in particular to the three genera Micromonas, Bathycoccus and Ostreococcus. These sequences originate mostly from coastal regions. Other groups with a large number of sequences include the Trebouxiophyceae, Chlorophyceae, Chlorodendrophyceae and Pyramimonadales. Some groups, such as the undescribed prasinophytes clades VII and IX, are mostly composed of environmental sequences. The 18S rRNA sequence database we assembled and validated should be useful for the analysis of metabarcode datasets acquired using next generation sequencing. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
2019 Project Peer Review
Functional Characterization of Cellular Metabolism U.S. Department of Energy (DOE) Bioenergy Technologies Office (BETO) 2019 Project Peer Review Advanced Algal Systems Scott Twary March 5, 2019 This presentation does not contain any proprietary, confidential, or otherwise restricted information Managed by Triad National Security, LLC for the U.S. Department of Energy’s NNSA LA-UR-19-20466 Goal Statement Goal Design an integrated strain improvement platform utilizing environmental, epigenetic, and genetic factors for targeted advances with rapid, comprehensive phenotyping leading to greater understanding of these modifications. Outcomes & Relevance Define the genetic pathway regulating nitrogen (N) sensing and signaling to produce an improved algae line with faster production due to rapid N assimilation and potentially uncouple N stress induction of lipid accumulation. Novel capability development • Integrated strain improvement strategy • Expanded suite of flow cytometry physiological assays • CRISPR/Cas genome engineering toolbox for Nannochloropsis salina • Epigenetic profiling and specific gene responses to environmental stress • EpiEffector modification and regulation of genome Los Alamos National Laboratory 3/05/19 | 2 Quad Chart Overview Barriers addressed Timeline: Ongoing Project Aft‐C. Biomass Genetics and • Current merit review period: Development: • October 1, 2017-September 30, 2020 • 33% complete Creation of novel integrated strain improvement methods and new tool applications. Total FY 17 FY 18 Total Costs Pre Costs Costs Planned Objective FY17** Funding (FY 19-Project To integrate flow cytometry, End Date) epigenome regulation, and genome engineering for elucidation of N DOE 2,200 K 650 K 1,100 K 1,334 K stress sensing and signaling and Funded application towards novel line improvement strategies Project Cost N/A End of Project Goal Share* An improved algae line with increased productivity over 30% of baseline. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, f g h i,j,k e Pavel Skaloud , Charles F. Delwiche , Andrew H. Knoll , John A. Raven , Heroen Verbruggen , Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2, and Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium; bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium; cVlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium; dBioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium; eSchool of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia; fDepartment of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic; gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742; hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom; jSchool of Biological Sciences, University of Western Australia, WA 6009, Australia; kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia; and lMeise Botanic Garden, 1860 Meise, Belgium Edited by Pamela S. Soltis, University of Florida, Gainesville, FL, and approved December 13, 2019 (received for review June 11, 2019) The Neoproterozoic Era records the transition from a largely clear interpretation of how many times and when green seaweeds bacterial to a predominantly eukaryotic phototrophic world, creat- emerged from unicellular ancestors (8). ing the foundation for the complex benthic ecosystems that have There is general consensus that an early split in the evolution sustained Metazoa from the Ediacaran Period onward. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected]. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
Comparing Relative Rates of Molecular Evolution Between Freshwater and Marine Eukaryotes
ORIGINAL ARTICLE doi:10.1111/evo.13000 Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes T. Fatima Mitterboeck,1,2,3 Alexander Y. Chen,1,2 Omar A. Zaheer,1,2 EddieY.T.Ma,1,2,4 and Sarah J. Adamowicz1,2 1Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario N1G 2W1, Canada 2Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada 3E-mail: [email protected] 4School of Computer Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada Received June 8, 2015 Accepted June 28, 2016 The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein-coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein-coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms. -
Diapositive 1
1 Diversity and ecology of green microalgae in marine systems: 2 an overview based on 18S rRNA sequences 3 4 Margot Tragin1, Adriana Lopes dos Santos1, Richard Christen2, 3, Daniel Vaulot1* 5 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Station Biologique, Place 6 Georges Teissier, 29680 Roscoff, France 7 2 CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice 8 cedex 02, France 9 3 Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc 10 Valrose, BP71. F06108 Nice cedex 02, France 11 12 13 * corresponding author : [email protected] 14 Revised version : 28 March 2016 15 For Perspectives in Phycology 16 17 Tragin et al. - Marine Chlorophyta diversity and distribution - p. 2 18 Abstract 19 Green algae (Chlorophyta) are an important group of microalgae whose diversity and ecological 20 importance in marine systems has been little studied. In this review, we first present an overview of 21 Chlorophyta taxonomy and detail the most important groups from the marine environment. Then, using 22 public 18S rRNA Chlorophyta sequences from culture and natural samples retrieved from the annotated 23 Protist Ribosomal Reference (PR²) database, we illustrate the distribution of different green algal 24 lineages in the oceans. The largest group of sequences belongs to the class Mamiellophyceae and in 25 particular to the three genera Micromonas, Bathycoccus and Ostreococcus. These sequences originate 26 mostly from coastal regions. Other groups with a large number of sequences include the 27 Trebouxiophyceae, Chlorophyceae, Chlorodendrophyceae and Pyramimonadales. Some groups, such as 28 the undescribed prasinophytes clades VII and IX, are mostly composed of environmental sequences. -
UNDERSTANDING the GENOMIC BASIS of STRESS ADAPTATION in PICOCHLORUM GREEN ALGAE by FATIMA FOFLONKER a Dissertation Submitted To
UNDERSTANDING THE GENOMIC BASIS OF STRESS ADAPTATION IN PICOCHLORUM GREEN ALGAE By FATIMA FOFLONKER A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Debashish Bhattacharya And approved by _________________________________________________ _________________________________________________ _________________________________________________ _________________________________________________ New Brunswick, New Jersey January 2018 ABSTRACT OF THE DISSERTATION Understanding the Genomic Basis of Stress Adaptation in Picochlorum Green Algae by FATIMA FOFLONKER Dissertation Director: Debashish Bhattacharya Gaining a better understanding of adaptive evolution has become increasingly important to predict the responses of important primary producers in the environment to climate-change driven environmental fluctuations. In my doctoral research, the genomes from four taxa of a naturally robust green algal lineage, Picochlorum (Chlorophyta, Trebouxiphycae) were sequenced to allow a comparative genomic and transcriptomic analysis. The over-arching goal of this work was to investigate environmental adaptations and the origin of haltolerance. Found in environments ranging from brackish estuaries to hypersaline terrestrial environments, this lineage is tolerant of a wide range of fluctuating salinities, light intensities, temperatures, and has a robust photosystem II. The small, reduced diploid genomes (13.4-15.1Mbp) of Picochlorum, indicative of genome specialization to extreme environments, has resulted in an interesting genomic organization, including the clustering of genes in the same biochemical pathway and coregulated genes. Coregulation of co-localized genes in “gene neighborhoods” is more prominent soon after exposure to salinity shock, suggesting a role in the rapid response to salinity stress in Picochlorum. -
Characterization of a Lipid-Producing Thermotolerant Marine Photosynthetic Pico-Alga in the Genus Picochlorum (Trebouxiophyceae)
European Journal of Phycology ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tejp20 Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae) Maja Mucko , Judit Padisák , Marija Gligora Udovič , Tamás Pálmai , Tihana Novak , Nikola Medić , Blaženka Gašparović , Petra Peharec Štefanić , Sandi Orlić & Zrinka Ljubešić To cite this article: Maja Mucko , Judit Padisák , Marija Gligora Udovič , Tamás Pálmai , Tihana Novak , Nikola Medić , Blaženka Gašparović , Petra Peharec Štefanić , Sandi Orlić & Zrinka Ljubešić (2020): Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae), European Journal of Phycology, DOI: 10.1080/09670262.2020.1757763 To link to this article: https://doi.org/10.1080/09670262.2020.1757763 View supplementary material Published online: 11 Aug 2020. Submit your article to this journal Article views: 11 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tejp20 British Phycological EUROPEAN JOURNAL OF PHYCOLOGY, 2020 Society https://doi.org/10.1080/09670262.2020.1757763 Understanding and using algae Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae) Maja Muckoa, Judit Padisákb, Marija Gligora Udoviča, Tamás Pálmai b,c, Tihana Novakd, Nikola Mediće, Blaženka Gašparovićb, Petra Peharec Štefanića, Sandi Orlićd and Zrinka Ljubešić a aUniversity of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia; bUniversity of Pannonia, Department of Limnology, Egyetem u. 10, 8200 Veszprém, Hungary; cDepartment of Plant Molecular Biology, Agricultural Institute, Centre for Agricultural Research, Brunszvik u.