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Shimakawa G, Shoguchi E, Burlacot A, Ifuku K, Che Y, Kumazawa M, Tanaka K, Nakanishi S. Coral symbionts evolved a functional polycistronic flavodiiron gene. PHOTOSYNTHESIS RESEARCH 2022; 151:113-124. [PMID: 34309771 DOI: 10.1007/s11120-021-00867-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/17/2021] [Indexed: 05/26/2023]
Abstract
Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2 photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized the FLV genes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is active in vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.
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Affiliation(s)
- Ginga Shimakawa
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Adrien Burlacot
- Aix Marseille University, CEA, CNRS, Institut de Biosciences Et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Kentaro Ifuku
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yufen Che
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Minoru Kumazawa
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Kenya Tanaka
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
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Zhang K, Zhang J, Ding N, Zellmer L, Zhao Y, Liu S, Liao DJ. ACTB and GAPDH appear at multiple SDS-PAGE positions, thus not suitable as reference genes for determining protein loading in techniques like Western blotting. Open Life Sci 2021; 16:1278-1292. [PMID: 34966852 PMCID: PMC8669867 DOI: 10.1515/biol-2021-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.
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Affiliation(s)
- Keyin Zhang
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Ju Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Nan Ding
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center , 730 South 8th St. , Minneapolis , MN 55415 , United States of America
| | - Yan Zhao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Siqi Liu
- Beijing Genomic Institute, Building 11 of Beishan Industrial Zone, Tantian District , Shengzhen 518083 , Guangdong Province , People’s Republic of China
| | - Dezhong Joshua Liao
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Department of Clinical Biochemistry, Guizhou Medical University Hospital , Guiyang 550004 , Guizhou Province , People’s Republic of China
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Kamikawa R, Yazaki E, Tahara M, Sakura T, Matsuo E, Nagamune K, Hashimoto T, Inagaki Y. Fates of Evolutionarily Distinct, Plastid-type Glyceraldehyde 3-phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates. J Eukaryot Microbiol 2018; 65:669-678. [PMID: 29478272 DOI: 10.1111/jeu.12512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 11/26/2022]
Abstract
The ancestral kareniacean dinoflagellate has undergone tertiary endosymbiosis, in which the original plastid is replaced by a haptophyte endosymbiont. During this plastid replacement, the endosymbiont genes were most likely flowed into the host dinoflagellate genome (endosymbiotic gene transfer or EGT). Such EGT may have generated the redundancy of functionally homologous genes in the host genome-one has resided in the host genome prior to the haptophyte endosymbiosis, while the other transferred from the endosymbiont genome. However, it remains to be well understood how evolutionarily distinct but functionally homologous genes were dealt in the dinoflagellate genomes bearing haptophyte-derived plastids. To model the gene evolution after EGT in plastid replacement, we here compared the characteristics of the two evolutionally distinct genes encoding plastid-type glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in Karenia brevis and K. mikimotoi bearing haptophyte-derived tertiary plastids: "gapC1h" acquired from the haptophyte endosymbiont and "gapC1p" inherited from the ancestral dinoflagellate. Our experiments consistently and clearly demonstrated that, in the two species examined, the principal plastid-type GAPDH is encoded by gapC1h rather than gapC1p. We here propose an evolutionary scheme resolving the EGT-derived redundancy of genes involved in plastid function and maintenance in the nuclear genomes of dinoflagellates that have undergone plastid replacements. Although K. brevis and K. mikimotoi are closely related to each other, the statuses of the two evolutionarily distinct gapC1 genes in the two Karenia species correspond to different steps in the proposed scheme.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Sciences and Graduate School of Human and Environmental Sciences, Kyoto University, Kyoto, Japan
| | - Euki Yazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Michiru Tahara
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaya Sakura
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Eriko Matsuo
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kisaburo Nagamune
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tetsuo Hashimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Liang MH, Jiang JG. Characterization and nitrogen deficiency response of ATP-citrate lyase from unicellular alga Dunaliella tertiolecta. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Nakayama T, Ishida KI, Archibald JM. Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion? PLoS One 2012; 7:e52340. [PMID: 23284996 PMCID: PMC3527533 DOI: 10.1371/journal.pone.0052340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/14/2012] [Indexed: 12/25/2022] Open
Abstract
Glycolysis is a central metabolic pathway in eukaryotic and prokaryotic cells. In eukaryotes, the textbook view is that glycolysis occurs in the cytosol. However, fusion proteins comprised of two glycolytic enzymes, triosephosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were found in members of the stramenopiles (diatoms and oomycetes) and shown to possess amino-terminal mitochondrial targeting signals. Here we show that mitochondrial TPI-GAPDH fusion protein genes are widely spread across the known diversity of stramenopiles, including non-photosynthetic species (Bicosoeca sp. and Blastocystis hominis). We also show that TPI-GAPDH fusion genes exist in three cercozoan taxa (Paulinella chromatophora, Thaumatomastix sp. and Mataza hastifera) and an apusozoan protist, Thecamonas trahens. Interestingly, subcellular localization predictions for other glycolytic enzymes in stramenopiles and a cercozoan show that a significant fraction of the glycolytic enzymes in these species have mitochondrial-targeted isoforms. These results suggest that part of the glycolytic pathway occurs inside mitochondria in these organisms, broadening our knowledge of the diversity of mitochondrial metabolism of protists.
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Affiliation(s)
- Takuro Nakayama
- Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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Ginger ML, McFadden GI, Michels PAM. Rewiring and regulation of cross-compartmentalized metabolism in protists. Philos Trans R Soc Lond B Biol Sci 2010; 365:831-45. [PMID: 20124348 DOI: 10.1098/rstb.2009.0259] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.
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Affiliation(s)
- Michael L Ginger
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK.
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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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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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Philippe H, Telford MJ. Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol 2006; 21:614-20. [PMID: 16919363 DOI: 10.1016/j.tree.2006.08.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 07/06/2006] [Accepted: 08/08/2006] [Indexed: 11/18/2022]
Abstract
Although comparisons of gene sequences have revolutionised our understanding of the animal phylogenetic tree, it has become clear that, to avoid errors in tree reconstruction, a large number of genes from many species must be considered: too few genes and stochastic errors predominate, too few taxa and systematic errors appear. We argue here that, to gather many sequences from many taxa, the best use of resources is to sequence a small number of expressed sequence tags (1000-5000 per species) from as many taxa as possible. This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Centre Robert-Cedergren, Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7.
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Waller RF, Patron NJ, Keeling PJ. Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra. Int J Syst Evol Microbiol 2006; 56:1439-1447. [PMID: 16738125 DOI: 10.1099/ijs.0.64061-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary history and relationship between plastids of dinoflagellate algae and apicomplexan parasites have been controversial both because the organelles are unusual and because their genomes contain few comparable genes. However, most plastid proteins are encoded in the host nucleus and targeted to the organelle, and several of these genes have proved to have interesting and informative evolutionary histories. We have used expressed sequence tag (EST) sequencing to generate gene sequence data from the nuclear genome of the dinoflagellate Heterocapsa triquetra and inferred phylogenies for the complete set of identified plastid-targeted proteins. Overall, dinoflagellate plastid proteins are most consistently related to homologues from the red algal plastid lineage (not green) and, in many of the most robust cases, they branch with other chromalveolate algae. In resolved phylogenies where apicomplexan data are available, dinoflagellates and apicomplexans are related. We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria.
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Affiliation(s)
- Ross F Waller
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Nicola J Patron
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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