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Slater B, Kosmützky D, Nisbet RER, Howe CJ. The Evolution of the Cytochrome c6 Family of Photosynthetic Electron Transfer Proteins. Genome Biol Evol 2021; 13:evab146. [PMID: 34165554 PMCID: PMC8358224 DOI: 10.1093/gbe/evab146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
During photosynthesis, electrons are transferred between the cytochrome b6f complex and photosystem I. This is carried out by the protein plastocyanin in plant chloroplasts, or by either plastocyanin or cytochrome c6 in many cyanobacteria and eukaryotic algal species. There are three further cytochrome c6 homologs: cytochrome c6A in plants and green algae, and cytochromes c6B and c6C in cyanobacteria. The function of these proteins is unknown. Here, we present a comprehensive analysis of the evolutionary relationship between the members of the cytochrome c6 family in photosynthetic organisms. Our phylogenetic analyses show that cytochromes c6B and c6C are likely to be orthologs that arose from a duplication of cytochrome c6, but that there is no evidence for separate origins for cytochromes c6B and c6C. We therefore propose renaming cytochrome c6C as cytochrome c6B. We show that cytochrome c6A is likely to have arisen from cytochrome c6B rather than by an independent duplication of cytochrome c6, and present evidence for an independent origin of a protein with some of the features of cytochrome c6A in peridinin dinoflagellates. We conclude with a new comprehensive model of the evolution of the cytochrome c6 family which is an integral part of understanding the function of the enigmatic cytochrome c6 homologs.
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Affiliation(s)
- Barnaby Slater
- Department of Biochemistry, University of Cambridge, United Kingdom
| | - Darius Kosmützky
- Department of Biochemistry, University of Cambridge, United Kingdom
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, United Kingdom
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2
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Morgan MB, Edge SE, Venn AA, Jones RJ. Developing transcriptional profiles in Orbicella franksi exposed to copper: Characterizing responses associated with a spectrum of laboratory-controlled environmental conditions. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 189:60-76. [PMID: 28599170 DOI: 10.1016/j.aquatox.2017.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/23/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Michael B Morgan
- Department of Biology, Berry College, School of Mathematics and Natural Sciences, 2277 Martha Berry Hwy, Mount Berry, GA, 30149, USA.
| | - Sara E Edge
- Hawaii Pacific University, 45-045 Kamehameha Hwy, Kaneohe, HI, 96744, USA
| | - Alexander A Venn
- Marine Biology Department et Laboratoire International Associé 647 "BIOSENSIB", Centre Scientifique de Monaco, 8 Quai Antoine 1er, MC98000, Monaco
| | - Ross J Jones
- Australian Institute of Marine Science (AIMS), Perth, 6009, Australia
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Markunas CM, Triemer RE. Evolutionary History of the Enzymes Involved in the Calvin–Benson Cycle in Euglenids. J Eukaryot Microbiol 2016; 63:326-39. [DOI: 10.1111/jeu.12282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Chelsea M. Markunas
- Department of Plant Biology Michigan State University 612 Wilson Road 166 Plant Biology Labs East Lansing Michigan 48824
| | - Richard E. Triemer
- Department of Plant Biology Michigan State University 612 Wilson Road 166 Plant Biology Labs East Lansing Michigan 48824
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Krueger T, Fisher PL, Becker S, Pontasch S, Dove S, Hoegh-Guldberg O, Leggat W, Davy SK. Transcriptomic characterization of the enzymatic antioxidants FeSOD, MnSOD, APX and KatG in the dinoflagellate genus Symbiodinium. BMC Evol Biol 2015; 15:48. [PMID: 25887897 PMCID: PMC4416395 DOI: 10.1186/s12862-015-0326-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/24/2015] [Indexed: 11/26/2022] Open
Abstract
Background The diversity of the symbiotic dinoflagellate Symbiodinium sp., as assessed by genetic markers, is well established. To what extent this diversity is reflected on the amino acid level of functional genes such as enzymatic antioxidants that play an important role in thermal stress tolerance of the coral-Symbiodinium symbiosis is, however, unknown. Here we present a predicted structural analysis and phylogenetic characterization of the enzymatic antioxidant repertoire of the genus Symbiodinium. We also report gene expression and enzymatic activity under short-term thermal stress in Symbiodinium of the B1 genotype. Results Based on eight different ITS2 types, covering six clades, multiple protein isoforms for three of the four investigated antioxidants (ascorbate peroxidase [APX], catalase peroxidase [KatG], manganese superoxide dismutase [MnSOD]) are present in the genus Symbiodinium. Amino acid sequences of both SOD metalloforms (Fe/Mn), as well as KatG, exhibited a number of prokaryotic characteristics that were also supported by the protein phylogeny. In contrast to the bacterial form, KatG in Symbiodinium is characterized by extended functionally important loops and a shortened C-terminal domain. Intercladal sequence variations were found to be much higher in both peroxidases, compared to SODs. For APX, these variable residues involve binding sites for substrates and cofactors, and might therefore differentially affect the catalytic properties of this enzyme between clades. While expression of antioxidant genes was successfully measured in Symbiodinium B1, it was not possible to assess the link between gene expression and protein activity due to high variability in expression between replicates, and little response in their enzymatic activity over the three-day experimental period. Conclusions The genus Symbiodinium has a diverse enzymatic antioxidant repertoire that has similarities to prokaryotes, potentially as a result of horizontal gene transfer or events of secondary endosymbiosis. Different degrees of sequence evolution between SODs and peroxidases might be the result of potential selective pressure on the conserved molecular function of SODs as the first line of defence. In contrast, genetic redundancy of hydrogen peroxide scavenging enzymes might permit the observed variations in peroxidase sequences. Our data and successful measurement of antioxidant gene expression in Symbiodinium will serve as basis for further studies of coral health. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0326-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Krueger
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand. .,Laboratory for Biological Geochemistry, ENAC, École polytechnique fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland.
| | - Paul L Fisher
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand. .,School of Civil Engineering, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Susanne Becker
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - Stefanie Pontasch
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - Sophie Dove
- School of Biological Sciences & ARC Centre of Excellence for Coral Reef Studies, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Ove Hoegh-Guldberg
- Global Change Institute, University of Queensland, Brisbane, QLD 4072, Australia.
| | - William Leggat
- Comparative Genomics Centre, School of Pharmacy and Molecular Sciences & ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
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Suescún-Bolívar LP, Iglesias-Prieto R, Thomé PE. Induction of glycerol synthesis and release in cultured Symbiodinium. PLoS One 2012; 7:e47182. [PMID: 23071753 PMCID: PMC3469543 DOI: 10.1371/journal.pone.0047182] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022] Open
Abstract
Background Symbiotic dinoflagellates transfer a substantial amount of their photosynthetic products to their animal hosts. This amount has been estimated to represent up to 90% of the photosynthetically fixed carbon and can satisfy in some instances the full respiratory requirements of the host. Although in several cnidarian-dinoflagellate symbioses glycerol is the primary photosynthetic product translocated to the host, the mechanism for its production and release has not been demonstrated conclusively. Principal Findings Using Symbiodinium cells in culture we were able to reproduce the synthesis and release of glycerol in vitro by employing an inductor for glycerol synthesis, osmotic up-shocks. Photosynthetic parameters and fluorescence analysis of photosystem II showed that the inductive conditions did not have a negative effect on photosynthetic performance, suggesting that the capacity for carbon fixation by the cells was not compromised. The demand for glycerol production required to attain osmotic balance increased the expression of ribulose 1,5-bisphosphate and of glycerol 3-phosphate dehydrogenase, possibly competing with the flux of fixed carbon necessary for protein synthesis. In longer exposures of cultured Symbiodinium cells to high osmolarity, the response was analogous to photoacclimation, reducing the excitation pressure over photosystem II, suggesting that Symbiodinium cells perceived the stress as an increase in light. The induced synthesis of glycerol resulted in a reduction of growth rates. Conclusions Our results favor a hypothetical mechanism of a signaling event involving a pressure sensor that may induce the flux of carbon (glycerol) from the symbiotic algae to the animal host, and strongly suggest that carbon limitation may be a key factor modulating the population of symbionts within the host.
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Affiliation(s)
- Luis P. Suescún-Bolívar
- Unidad Académica de Sistemas Arrecifales Puerto Morelos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Roberto Iglesias-Prieto
- Unidad Académica de Sistemas Arrecifales Puerto Morelos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Patricia E. Thomé
- Unidad Académica de Sistemas Arrecifales Puerto Morelos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail:
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Pochon X, Putnam HM, Burki F, Gates RD. Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus Symbiodinium. PLoS One 2012; 7:e29816. [PMID: 22238660 PMCID: PMC3251599 DOI: 10.1371/journal.pone.0029816] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/06/2011] [Indexed: 11/28/2022] Open
Abstract
Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A-I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A-H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A-H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.
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Affiliation(s)
- Xavier Pochon
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i, Kane'ohe, Hawai'i, United States of America.
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Stat M, Baker AC, Bourne DG, Correa AMS, Forsman Z, Huggett MJ, Pochon X, Skillings D, Toonen RJ, van Oppen MJH, Gates RD. Molecular delineation of species in the coral holobiont. ADVANCES IN MARINE BIOLOGY 2012; 63:1-65. [PMID: 22877610 DOI: 10.1016/b978-0-12-394282-1.00001-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The coral holobiont is a complex assemblage of organisms spanning a diverse taxonomic range including a cnidarian host, as well as various dinoflagellate, prokaryotic and acellular symbionts. With the accumulating information on the molecular diversity of these groups, binomial species classification and a reassessment of species boundaries for the partners in the coral holobiont is a logical extension of this work and will help enhance the capacity for comparative research among studies. To aid in this endeavour, we review the current literature on species diversity for the three best studied partners of the coral holobiont (coral, Symbiodinium, prokaryotes) and provide suggestions for future work on systematics within these taxa. We advocate for an integrative approach to the delineation of species using both molecular genetics in combination with phenetic characters. We also suggest that an a priori set of criteria be developed for each taxonomic group as no one species concept or accompanying set of guidelines is appropriate for delineating all members of the coral holobiont.
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Affiliation(s)
- Michael Stat
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii, Kaneohe, HI, USA.
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López-Legentil S, Song B, DeTure M, Baden DG. Characterization and localization of a hybrid non-ribosomal peptide synthetase and polyketide synthase gene from the toxic dinoflagellate Karenia brevis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:32-41. [PMID: 19468793 DOI: 10.1007/s10126-009-9197-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 04/21/2009] [Indexed: 05/27/2023]
Abstract
The toxic dinoflagellate Karenia brevis, a causative agent of the red tides in Florida, produces a series of toxic compounds known as brevetoxins and their derivatives. Recently, several putative genes encoding polyketide synthase (PKS) were identified from K. brevis in an effort to elucidate the genetic systems involved in brevetoxin production. In this study, novel PKS sequences were isolated from three clones of K. brevis. Eighteen unique sequences were obtained for the PKS ketosynthase (KS) domain of K. brevis. Phylogenetic comparison with closely related PKS genes revealed that 16 grouped with cyanobacteria sequences, while the remaining two grouped with Apicomplexa and previously reported sequences for K. brevis. A fosmid library was also constructed to further characterize PKS genes detected in K. brevis Wilson clone. Several fosmid clones were positive for the presence of PKS genes, and one was fully sequenced to determine the full structure of the PKS cluster. A hybrid non ribosomal peptide synthetase and PKS (NRPS-PKS) gene cluster of 16,061 bp was isolated. In addition, we assessed whether the isolated gene was being actively expressed using reverse transcription polymerase chain reaction (RT-PCR) and determined its localization at the cellular level by chloroplast isolation. RT-PCR analyses revealed that this gene was actively expressed in K. brevis cultures. The hybrid NRPS-PKS gene cluster was located in the chloroplast, suggesting that K. brevis acquired the ability to produce some of its secondary metabolites through endosymbiosis with ancestral cyanobacteria. Further work is needed to determine the compound produced by the NRPS-PKS hybrid, to find other PKS gene sequences, and to assess their role in K. brevis toxin biosynthetic pathway.
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Affiliation(s)
- Susanna López-Legentil
- Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA.
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Dang Y, Green BR. Long transcripts from dinoflagellate chloroplast minicircles suggest "rolling circle" transcription. J Biol Chem 2009; 285:5196-203. [PMID: 19948728 DOI: 10.1074/jbc.m109.058545] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The chloroplast genome of a dinoflagellate consists of a group of small circular DNA molecules (minicircles), most of which carry a single gene. With RT-PCR, primer extension, and Northern analyses, we show that the entire minicircle is transcribed and that some minicircles can produce RNAs larger than themselves. Using an RNA ligase-mediated rapid amplification of cDNA ends method, we were able to detect large processed precursors that are generated by endonucleolytic cleavage of an even longer molecule. This cleavage produces the mature mRNA 3'-end and at the same time the 5'-end of the precursor. The tRNAs encoded by the petD and psbE minicircles appear to be processed in the same way. We propose a "rolling circle" model for chloroplast transcription in which transcription would proceed continuously around the minicircular DNA to produce transcripts larger than the minicircle itself. These transcripts would be further processed into discrete mature mRNAs and tRNAs.
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Affiliation(s)
- Yunkun Dang
- Botany Department, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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Takishita K, Yamaguchi H, Maruyama T, Inagaki Y. A hypothesis for the evolution of nuclear-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase genes in "chromalveolate" members. PLoS One 2009; 4:e4737. [PMID: 19270733 PMCID: PMC2649427 DOI: 10.1371/journal.pone.0004737] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 02/05/2009] [Indexed: 11/18/2022] Open
Abstract
Eukaryotes bearing red alga-derived plastids — photosynthetic alveolates (dinoflagellates plus the apicomplexan Toxoplasma gondii plus the chromerid Chromera velia), photosynthetic stramenopiles, haptophytes, and cryptophytes — possess unique plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (henceforth designated as “GapC1”). Pioneering phylogenetic studies have indicated a single origin of the GapC1 enzymes in eukaryotic evolution, but there are two potential idiosyncrasies in the GapC1 phylogeny: Firstly, the GapC1 tree topology is apparently inconsistent with the organismal relationship among the “GapC1-containing” groups. Secondly, four stramenopile GapC1 homologues are consistently paraphyletic in previously published studies, although these organisms have been widely accepted as monophyletic. For a closer examination of the above issues, in this study GapC1 gene sampling was improved by determining/identifying nine stramenopile and two cryptophyte genes. Phylogenetic analyses of our GapC1 dataset, which is particularly rich in the stramenopile homologues, prompt us to propose a new scenario that assumes multiple, lateral GapC1 gene transfer events to explain the incongruity between the GapC1 phylogeny and the organismal relationships amongst the “GapC1-containing” groups. Under our new scenario, GapC1 genes uniquely found in photosynthetic alveolates, photosynthetic stramenopiles, haptophytes, and cryptopyhytes are not necessarily a character vertically inherited from a common ancestor.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan.
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Keeling PJ. Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. Methods Mol Biol 2009; 532:501-515. [PMID: 19271204 DOI: 10.1007/978-1-60327-853-9_29] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plastids are the organelles derived from a cyanobacterium through endosymbiosis. Unlike mitochondria, plastids are not found in all eukaryotes, but their evolution has an added layer of complexity since plastids have moved between eukaryotic lineages by secondary and tertiary endosymbiotic events. This complex history, together with the genetic integration between plastids and their host, has led to many opportunities for gene flow between phylogenetically distinct lineages. Some intracellular transfers do not lead to a protein functioning in a new environment, but many others do and the protein makeup of many plastids appears to have been influenced by exogenous sources as well. Here, different evolutionary sources and cellular destinations of gene flow that has affected the plastid lineage are reviewed. Most horizontal gene transfer (HGT) affecting the modern plastid has taken place via the host nucleus, in the form of genes for plastid-targeted proteins. The impact of this varies greatly from lineage to lineage, but in some cases such transfers can be as high as one fifth of analyzed genes. More rarely, genes have also been transferred to the plastid genome itself, and plastid genes have also been transferred to other non-plant, non-algal lineages. Overall, the proteome of many plastids has emerged as a mosaic of proteins from many sources, some from within the same cell (e.g., cytosolic genes or genes left over from the replacement of an earlier plastid), some from the plastid of other algal lineages, and some from completely unrelated sources.
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Affiliation(s)
- Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
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Oborník M, Janouškovec J, Chrudimský T, Lukeš J. Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again. Int J Parasitol 2009; 39:1-12. [DOI: 10.1016/j.ijpara.2008.07.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/23/2008] [Accepted: 07/25/2008] [Indexed: 10/21/2022]
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Kim E, Archibald JM. Diversity and Evolution of Plastids and Their Genomes. PLANT CELL MONOGRAPHS 2008. [DOI: 10.1007/978-3-540-68696-5_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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SANCHEZ-PEREZ GABINOF, HAMPL VLADIMIR, SIMPSON ALASTAIRGB, ROGER ANDREWJ. A New Divergent Type of Eukaryotic Methionine Adenosyltransferase is Present in Multiple Distantly Related Secondary Algal Lineages. J Eukaryot Microbiol 2008; 55:374-81. [DOI: 10.1111/j.1550-7408.2008.00349.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution. Gene 2008; 441:22-7. [PMID: 18420358 DOI: 10.1016/j.gene.2008.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 03/04/2008] [Indexed: 11/20/2022]
Abstract
Although lateral gene transfer (LGT) events have been frequently documented in the evolution of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), no eukaryote-to-prokaryote transfer has been reported so far. Here we describe the first case of the GAPDH gene transfer from a eukaryote to a subset of Clostridium species (Bacteria, Firmicutes). A series of phylogenetic analyses of GAPDH homologues revealed that Clostridium thermocellum and Clostridium cellulolyticum homologues have the evolutionary affinity to the eukaryotic homologues, rather than to those of bacterial species closely related to the two Clostridium species in the organismal phylogeny. These results suggest that the GAPDH genes in the two Clostridium species are of eukaryotic origin, which is the first reported case of eukaryote-to-bacterium GAPDH gene transfer. Since a previously published 16S ribosomal DNA phylogeny and our GAPDH phylogeny commonly suggest an intimate evolutionary relationship between C. thermocellum and C. cellulolyticum, a common ancestor of the two species likely acquired the eukaryotic GAPDH gene. In the C. cellulolyticum genome, the exogenous GAPDH gene was physically separated from other glycolytic genes, suggesting that this gene organization was likely achieved by a random insertion of the laterally transferred gene. On the other hand, in the C. thermocellum genome, the laterally transferred GAPDH gene clusters with other bacterial glycolytic genes. We discuss possible scenarios for the evolutionarily chimeric glycolytic gene cluster in the C. thermocellum genome.
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Takishita K, Kawachi M, Noël MH, Matsumoto T, Kakizoe N, Watanabe MM, Inouye I, Ishida KI, Hashimoto T, Inagaki Y. Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene 2007; 410:26-36. [PMID: 18191504 DOI: 10.1016/j.gene.2007.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 11/12/2007] [Accepted: 11/19/2007] [Indexed: 10/22/2022]
Abstract
The dinoflagellate Lepidodinium chlorophorum possesses "green" plastids containing chlorophylls a and b (Chl a+b), unlike most dinoflagellate plastids with Chl a+c plus a carotenoid peridinin (peridinin-containing plastids). In the present study we determined 8 plastid-encoded genes from Lepidodinium to investigate the origin of the Chl a+b-containing dinoflagellate plastids. The plastid-encoded gene phylogeny clearly showed that Lepidodinium plastids were derived from a member of Chlorophyta, consistent with pigment composition. We also isolated three different glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes from Lepidodinium-one encoding the putative cytosolic "GapC" enzyme and the remaining two showing affinities to the "plastid-targeted GapC" genes. In a GAPDH phylogeny, one of the plastid-targeted GapC-like sequences robustly grouped with those of dinoflagellates bearing peridinin-containing plastids, while the other was nested in a clade of the homologues of haptophytes and dinoflagellate genera Karenia and Karlodinium bearing "haptophyte-derived" plastids. Since neither host nor plastid phylogeny suggested an evolutionary connection between Lepidodinium and Karenia/Karlodinium, a lateral transfer of a plastid-targeted GapC gene most likely took place from a haptophyte or a dinoflagellate with haptophyte-derived plastids to Lepidodinium. The plastid-targeted GapC data can be considered as an evidence for the single origin of plastids in haptophytes, cryptophytes, stramenopiles, and alveolates. However, in the light of Lepidodinium GAPDH data, we need to closely examine whether the monophyly of the plastids in the above lineages inferred from plastid-targeted GapC genes truly reflects that of the host lineages.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Nosenko T, Bhattacharya D. Horizontal gene transfer in chromalveolates. BMC Evol Biol 2007; 7:173. [PMID: 17894863 PMCID: PMC2064935 DOI: 10.1186/1471-2148-7-173] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 09/25/2007] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT), the non-genealogical transfer of genetic material between different organisms, is considered a potentially important mechanism of genome evolution in eukaryotes. Using phylogenomic analyses of expressed sequence tag (EST) data generated from a clonal cell line of a free living dinoflagellate alga Karenia brevis, we investigated the impact of HGT on genome evolution in unicellular chromalveolate protists. RESULTS We identified 16 proteins that have originated in chromalveolates through ancient HGTs before the divergence of the genera Karenia and Karlodinium and one protein that was derived through a more recent HGT. Detailed analysis of the phylogeny and distribution of identified proteins demonstrates that eight have resulted from independent HGTs in several eukaryotic lineages. CONCLUSION Recurring intra- and interdomain gene exchange provides an important source of genetic novelty not only in parasitic taxa as previously demonstrated but as we show here, also in free-living protists. Investigating the tempo and mode of evolution of horizontally transferred genes in protists will therefore advance our understanding of mechanisms of adaptation in eukaryotes.
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Affiliation(s)
- Tetyana Nosenko
- University of Iowa, Department of Biological Sciences and the Roy J. Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, Iowa 52242, USA
| | - Debashish Bhattacharya
- University of Iowa, Department of Biological Sciences and the Roy J. Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, Iowa 52242, USA
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A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol Biol 2007; 7:89. [PMID: 17562012 PMCID: PMC1920508 DOI: 10.1186/1471-2148-7-89] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 06/11/2007] [Indexed: 11/13/2022] Open
Abstract
Background Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common observation interpreted in this way is the appearance of a bacterial gene (one that is not clearly derived from the mitochondrion or plastid) in a eukaryotic nuclear genome. Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage. Results Here we show that several apparently simple cases of lateral transfer are actually more complex than they originally appeared: in these instances we find that two or more distantly related eukaryotic groups share the same bacterial gene, resulting in a punctate distribution. Specifically, we describe phylogenies of three core carbon metabolic enzymes: transketolase, glyceraldehyde-3-phosphate dehydrogenase and ribulose-5-phosphate-3-epimerase. Phylogenetic trees of each of these enzymes includes a strongly-supported clade consisting of several eukaryotes that are distantly related at the organismal level, but whose enzymes are apparently all derived from the same lateral transfer. With less sampling any one of these examples would appear to be a simple case of bacterium-to-eukaryote lateral transfer; taken together, their evolutionary histories cannot be so simple. The distributions of these genes may represent ancient paralogy events or genes that have been transferred from bacteria to an ancient ancestor of the eukaryotes that retain them. They may alternatively have been transferred laterally from a bacterium to a single eukaryotic lineage and subsequently transferred between distantly related eukaryotes. Conclusion Determining how complex the distribution of a transferred gene is depends on the sampling available. These results show that seemingly simple cases may be revealed to be more complex with greater sampling, suggesting many bacterial genes found in eukaryotic genomes may have a punctate distribution.
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Grauvogel C, Petersen J. Isoprenoid biosynthesis authenticates the classification of the green alga Mesostigma viride as an ancient streptophyte. Gene 2007; 396:125-33. [PMID: 17433859 DOI: 10.1016/j.gene.2007.02.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 02/23/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
Land plants harbor two essential and completely different metabolic pathways for isoprenoid synthesis. The cytosolic mevalonate pathway (MVA) is shared with heterotrophic eukaryotes, whereas the plastidial 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway has a cyanobacterial origin and was recruited after primary endosymbiosis. Terrestrial plants and green algae have a common evolutionary ancestry, but biochemical as well as genome analyses indicate that the cytosolic MVA pathway is generally absent from Chlorophyta. We investigated the distribution of genes for both pathways in the green alga Mesostigma viride, a key species at the basis of streptophycean (charophycean green algae, land plant) evolution. Ten of altogether twelve generally weakly expressed genes for isoprenoid biosynthesis, including three for the cytosolic MVA pathway, were amplified using a reverse transcription PCR approach with individually designed degenerate primers. Two full length cDNA clones for the first enzyme of the MVA pathway (HMGS) were additionally established from the charophycean green alga Chara vulgaris by library screening. The presence of the MVA pathway in these advanced green algae indicates a universal distribution among Streptophyta, and our phylogenetic HMGS analyses substantiate the recent classification of Mesostigma basal to charophytes and land plants. We identified each of the five cytosolic MVA genes/cDNAs in the genome of the rhodophyte Galdieria sulphuraria and, furthermore, amplified four of them from the glaucophyte Cyanophora paradoxa. Our data indicate that the MVA pathway is a characteristic trait of Plantae in general and propose that it was specifically lost in a common ancestor of Chlorophyta.
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Affiliation(s)
- Carina Grauvogel
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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21
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Abstract
Oomycetes and filamentous parasitic fungi are plant pathogens that have undergone convergent evolution. A recent study has shown that these microbial eukaryotes have exchanged metabolic genes, which might explain some of their phenotypic similarities.
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Affiliation(s)
- Jan O Andersson
- Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-751 24 Uppsala, Sweden.
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22
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Andersson JO, Hirt RP, Foster PG, Roger AJ. Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol 2006; 6:27. [PMID: 16551352 PMCID: PMC1484493 DOI: 10.1186/1471-2148-6-27] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 03/21/2006] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. RESULTS The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. CONCLUSION Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
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Affiliation(s)
- Jan O Andersson
- Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-751 24 Uppsala, Sweden
| | - Robert P Hirt
- School of Biology, The Devonshire Building, The University of Newcastle upon Tyne, NE1 7RU, UK
| | - Peter G Foster
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andrew J Roger
- The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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Petersen J, Teich R, Brinkmann H, Cerff R. A “Green” Phosphoribulokinase in Complex Algae with Red Plastids: Evidence for a Single Secondary Endosymbiosis Leading to Haptophytes, Cryptophytes, Heterokonts, and Dinoflagellates. J Mol Evol 2006; 62:143-57. [PMID: 16474987 DOI: 10.1007/s00239-004-0305-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Accepted: 05/24/2005] [Indexed: 01/06/2023]
Abstract
Phosphoribulokinase (PRK) is an essential enzyme of photosynthetic eukaryotes which is active in the plastid-located Calvin cycle and regenerates the substrate for ribulose-bisphosphate carboxylase/oxygenase (Rubisco). Rhodophytes and chlorophytes (red and green algae) recruited their nuclear-encoded PRK from the cyanobacterial ancestor of plastids. The plastids of these organisms can be traced back to a single primary endosymbiosis, whereas, for example, haptophytes, dinoflagellates, and euglenophytes obtained their "complex" plastids through secondary endosymbioses, comprising the engulfment of a unicellular red or green alga by a eukaryotic host cell. We have cloned eight new PRK sequences from complex algae as well as a rhodophyte in order to investigate their evolutionary origin. All available PRK sequences were used for phylogenetic analyses and the significance of alternative topologies was estimated by the approximately unbiased test. Our analyses led to several astonishing findings. First, the close relationship of PRK genes of haptophytes, heterokontophytes, cryptophytes, and dinophytes (complex red lineage) supports a monophyletic origin of their sequences and hence their plastids. Second, based on PRK genes the complex red lineage forms a highly supported assemblage together with chlorophytes and land plants, to the exclusion of the rhodophytes. This green affinity is in striking contrast to the expected red algal origin and our analyses suggest that the PRK gene was acquired once via lateral transfer from a green alga. Third, surprisingly the complex green lineages leading to Bigelowiella and Euglena probably also obtained their PRK genes via lateral gene transfers from a red alga and a complex alga with red plastids, respectively.
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Affiliation(s)
- Jörn Petersen
- Institut für Genetik, Technische Universität Braunschweig, D-38106, Braunschweig, Germany.
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Takishita K, Patron NJ, Ishida KI, Maruyama T, Keeling PJ. A Transcriptional Fusion of Genes Encoding Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and Enolase in Dinoflagellates. J Eukaryot Microbiol 2005; 52:343-8. [PMID: 16014012 DOI: 10.1111/j.1550-7408.2005.00042x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and enolase are enzymes essential for glycolysis and gluconeogenesis. Dinoflagellates possess several types of both GAPDH and enolase genes. Here, we identify a novel cytosolic GAPDH-enolase fusion protein in several dinoflagellate species. Phylogenetic analyses revealed that the GAPDH moiety of this fusion is weakly related to a cytosolic GAPDH previously reported in dinoflagellates, ciliates, and an apicomplexan. The enolase moiety has phylogenetic affinity with sequences from ciliates and apicomplexans, as expected for dinoflagellate genes. Furthermore, the enolase moiety has two insertions in a highly conserved region of the gene that are shared with ciliate and apicomplexan homologues, as well as with land plants, stramenopiles, haptophytes, and a chlorarachniophyte. Another glycolytic gene fusion in eukaryotes is the mitochondrion-targeted triose-phosphate isomerase (TPI) and GAPDH fusion in stramenopiles (i.e. diatoms and oomycetes). However, unlike the mitochondrial TPI-GAPDH fusion, the GAPDH-enolase fusion protein appears to exist in the same compartment as stand-alone homologues of each protein, and the metabolic reactions they catalyze in glycolysis and gluconeogenesis are not directly sequential. It is possible that the fusion is post-translationally processed to give separate GAPDH and enolase products, or that the fusion protein may function as a single bifunctional polypeptide in glycolysis, gluconeogenesis, or perhaps more likely in some previously unrecognized metabolic capacity.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.
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Grzebyk D, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O, Taylor FJR, Falkowski PG. Response to Comment on "The Evolution of Modern Eukaryotic Phytoplankton". Science 2004. [DOI: 10.1126/science.1105297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Daniel Grzebyk
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA
| | - Miriam E. Katz
- Department of Geological Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andrew H. Knoll
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Antonietta Quigg
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - John A. Raven
- Division of Environmental and Applied Biology, University of Dundee at SCRI, Scottish Crop Research Institute, Inergowrie, Dundee DD2 5DA, UK
| | - Oscar Schofield
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - F. J. R. Taylor
- Department of Earth and Ocean Science and Department of Botany, University of British Columbia, 270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ and Department of Geological Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ
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