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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Kim JI, Jo BY, Park MG, Yoo YD, Shin W, Archibald JM. Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:896138. [PMID: 35769291 PMCID: PMC9235467 DOI: 10.3389/fpls.2022.896138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Bok Yeon Jo
- Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
| | - Yeong Du Yoo
- Department of Marine Biology, College of Ocean Sciences and Technology, Kunsan National University, Kunsan, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Recent Progress in the Study of Peroxiredoxin in the Harmful Algal Bloom Species Chattonella marina. Antioxidants (Basel) 2021; 10:antiox10020162. [PMID: 33499182 PMCID: PMC7911785 DOI: 10.3390/antiox10020162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Peroxiredoxin (Prx) is a relatively recently discovered antioxidant enzyme family that scavenges peroxides and is known to be present in organisms from biological taxa ranging from bacteria to multicellular eukaryotes, including photosynthetic organisms. Although there have been many studies of the Prx family in higher plants, green algae, and cyanobacteria, few studies have concerned raphidophytes and dinoflagellates, which are among the eukaryotic algae that cause harmful algal blooms (HABs). In our proteomic study using 2-D electrophoresis, we found a highly expressed 2-Cys peroxiredoxin (2-CysPrx) in the raphidophyte Chattonella marina var. antiqua, a species that induces mass mortality of aquacultured fish. The abundance of the C. marina 2-CysPrx enzyme was highest in the exponential growth phase, during which photosynthetic activity was high, and it then decreased by about a factor of two during the late stationary growth phase. This pattern suggested that 2-CysPrx is a key enzyme involved in the maintenance of high photosynthesis activity. In addition, the fact that the depression of photosynthesis by excessively high irradiance was more severe in the 2-CysPrx low-expression strain (wild type) than in the normal-expression strain (wild type) of C. marina suggested that 2-CysPrx played a critical role in protecting the cell from oxidative stress caused by exposure to excessively high irradiance. In the field of HAB research, estimates of growth potential have been desired to predict the population dynamics of HABs for mitigating damage to fisheries. Therefore, omics approaches have recently begun to be applied to elucidate the physiology of the growth of HAB species. In this review, we describe the progress we have made using a molecular physiological approach to identify the roles of 2-CysPrx and other antioxidant enzymes in mitigating environmental stress associated with strong light and high temperatures and resultant oxidative stress. We also describe results of a survey of expressed Prx genes and their growth-phase-dependent behavior in C. marina using RNA-seq analysis. Finally, we speculate about the function of these genes and the ecological significance of 2-CysPrx, such as its involvement in circadian rhythms and the toxicity of C. marina to fish.
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Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
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Deodato CR, Barlow SB, Hovde BT, Cattolico RA. Naked Chrysochromulina (Haptophyta) isolates from lake and river ecosystems: An electron microscopic comparison including new observations on the type species of this taxon. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes. Genes (Basel) 2019; 10:genes10030245. [PMID: 30909525 PMCID: PMC6471398 DOI: 10.3390/genes10030245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 11/30/2022] Open
Abstract
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes.
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Figueroa-Martinez F, Jackson C, Reyes-Prieto A. Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity. Genome Biol Evol 2019; 11:174-188. [PMID: 30534986 PMCID: PMC6330054 DOI: 10.1093/gbe/evy268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Plastid genome (ptDNA) data of Glaucophyta have been limited for many years to the genus Cyanophora. Here, we sequenced the ptDNAs of Gloeochaete wittrockiana, Cyanoptyche gloeocystis, Glaucocystis incrassata, and Glaucocystis sp. BBH. The reported sequences are the first genome-scale plastid data available for these three poorly studied glaucophyte genera. Although the Glaucophyta plastids appear morphologically “ancestral,” they actually bear derived genomes not radically different from those of red algae or viridiplants. The glaucophyte plastid coding capacity is highly conserved (112 genes shared) and the architecture of the plastid chromosomes is relatively simple. Phylogenomic analyses recovered Glaucophyta as the earliest diverging Archaeplastida lineage, but the position of viridiplants as the first branching group was not rejected by the approximately unbiased test. Pairwise distances estimated from 19 different plastid genes revealed that the highest sequence divergence between glaucophyte genera is frequently higher than distances between species of different classes within red algae or viridiplants. Gene synteny and sequence similarity in the ptDNAs of the two Glaucocystis species analyzed is conserved. However, the ptDNA of Gla. incrassata contains a 7.9-kb insertion not detected in Glaucocystis sp. BBH. The insertion contains ten open reading frames that include four coding regions similar to bacterial serine recombinases (two open reading frames), DNA primases, and peptidoglycan aminohydrolases. These three enzymes, often encoded in bacterial plasmids and bacteriophage genomes, are known to participate in the mobilization and replication of DNA mobile elements. It is therefore plausible that the insertion in Gla. incrassata ptDNA is derived from a DNA mobile element.
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Affiliation(s)
- Francisco Figueroa-Martinez
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,CONACyT-Universidad Autónoma Metropolitana Iztapalapa, Biotechnology Department, Mexico City, Mexico
| | - Christopher Jackson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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Hovde BT, Deodato CR, Andersen RA, Starkenburg SR, Barlow SB, Cattolico RA. Chrysochromulina: Genomic assessment and taxonomic diagnosis of the type species for an oleaginous algal clade. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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The first plastid genome of a filamentous taxon 'Bangia' sp. OUCPT-01 in the Bangiales. Sci Rep 2018; 8:10688. [PMID: 30013114 PMCID: PMC6048033 DOI: 10.1038/s41598-018-29083-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/02/2018] [Indexed: 11/22/2022] Open
Abstract
Red algae are important primary photosynthetic organisms. The Bangiales comprise a morphologically diverse order of red algae. Until now, complete plastid genomes of the Bangiales were only mapped for foliose species. To date, no filamentous plastomes have been published. The aim of this study was to determine and analyze the complete plastid genome of the filamentous marine species ‘Bangia’ sp. OUCPT-01. It is a circular molecule, 196,913 bps in length with a guanine-cytosine (GC) content of 33.5%. It has a quadripartite structure with two single copy regions separated by two direct non-identical repeats. It has 205 protein-coding genes, 37 tRNAs, and 6 rRNAs. Therefore, it has a high coding capacity and is highly similar to other Bangiales species in terms of content and structure. In particular, it reveals that the genera in the Bangiales have highly conserved gene content and plastome synteny. This plastome and existing data provide insights into the phylogenetic relationships among the Bangiales genera of the Rhodophyta. According to its plastid- and mitochondrial genomes, ‘Bangia 2′ is a sister group to Porphyra. However, the position of Wildemania schizophylla in the Bangiales is still controversial. Our results show that the Bangiales divergence time was ~225 million years ago.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
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Liu F, Jin Z, Wang Y, Bi Y, Melton JT. Plastid Genome of Dictyopteris divaricata (Dictyotales, Phaeophyceae): Understanding the Evolution of Plastid Genomes in Brown Algae. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:627-637. [PMID: 29164355 DOI: 10.1007/s10126-017-9781-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/05/2017] [Indexed: 06/07/2023]
Abstract
Dictyotophycidae is a subclass of brown algae containing 395 species that are distributed worldwide. A complete plastid (chloroplast) genome (ptDNA or cpDNA) had not previously been sequenced from this group. In this study, the complete plastid genome of Dictyopteris divaricata (Okamura) Okamura (Dictyotales, Phaeophyceae) was characterized and compared to other brown algal ptDNAs. This plastid genome was 126,099 bp in size with two inverted repeats (IRs) of 6026 bp. The D. divaricata IRs contained rpl21, making its IRs larger than representatives from the orders Fucales and Laminariales, but was smaller than that from Ectocarpales. The G + C content of D. divaricata (31.19%) was the highest of the known ptDNAs of brown algae (28.94-31.05%). Two protein-coding genes, rbcR and rpl32, were present in ptDNAs of Laminariales, Ectocarpales (Ectocarpus siliculosus), and Fucales (LEF) but were absent in D. divaricata. Reduced intergenic space (13.11%) and eight pairs of overlapping genes in D. divaricata ptDNA made it the most compact plastid genome in brown algae so far. The architecture of D. divaricata ptDNA showed higher similarity to that of Laminariales compared with Fucales and Ectocarpales. The difference in general features, gene content, and architecture among the ptDNAs of D. divaricata and LEF clade revealed the diversity and evolutionary trends of plastid genomes in brown algae.
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Affiliation(s)
- Feng Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, People's Republic of China.
| | - Zhe Jin
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, People's Republic of China
- College of Life Science, Shandong Normal University, Jinan, Shandong, 250014, People's Republic of China
| | - Yu Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, People's Republic of China
- School of Life Sciences, Shandong University, Jinan, Shandong, 250100, People's Republic of China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China
| | - James T Melton
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487-0345, USA
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Chloroplast Genome Sequences of Seven Strains of the Bloom-Forming Raphidophyte Heterosigma akashiwo. GENOME ANNOUNCEMENTS 2017; 5:5/41/e01030-17. [PMID: 29025932 PMCID: PMC5637492 DOI: 10.1128/genomea.01030-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the complete chloroplast genome sequences of seven strains of the bloom-forming raphidophyte Heterosigma akashiwo. These ~160-kb sequences contain 124 protein-, 6 rRNA-, and 34 tRNA-coding sequences. Notable sequence variations were observed among these seven sequenced and two previously characterized strains.
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Dabbagh N, Bennett MS, Triemer RE, Preisfeld A. Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis. PeerJ 2017; 5:e3725. [PMID: 28852596 PMCID: PMC5572947 DOI: 10.7717/peerj.3725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of Eutreptiella pomquetensis, and the spread and peculiarities of introns. METHODS The Etl. pomquetensis cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including Pyramimonas parkeae. RESULTS AND DISCUSSION With about 130,561 bp the chloroplast genome of Etl. pomquetensis, a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in Etl. pomquetensis was completely different from those observed in green algae and plants. The gene composition of Etl. pomquetensis was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to P. parkeae. Furthermore, the cpGenome of Etl. pomquetensis was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of Etl. pomquetensis showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III introns are degenerated group II introns and evolved later.
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Affiliation(s)
- Nadja Dabbagh
- Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Bergische Universität Wuppertal, Wuppertal, Germany
| | - Matthew S Bennett
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Richard E Triemer
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Angelika Preisfeld
- Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Bergische Universität Wuppertal, Wuppertal, Germany
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Muñoz-Gómez SA, Mejía-Franco FG, Durnin K, Colp M, Grisdale CJ, Archibald JM, Slamovits CH. The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Curr Biol 2017; 27:1677-1684.e4. [DOI: 10.1016/j.cub.2017.04.054] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022]
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Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Bhattacharya D, Yoon HS. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biol 2016; 14:75. [PMID: 27589960 PMCID: PMC5010701 DOI: 10.1186/s12915-016-0299-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Suk Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Lyubetsky V, Gershgorin R, Seliverstov A, Gorbunov K. Algorithms for reconstruction of chromosomal structures. BMC Bioinformatics 2016; 17:40. [PMID: 26780836 PMCID: PMC4717669 DOI: 10.1186/s12859-016-0878-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem. RESULTS A general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model. CONCLUSIONS Exactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable.
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Affiliation(s)
- Vassily Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetnyi lane, 19, 127051, Moscow, Russia.
| | - Roman Gershgorin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetnyi lane, 19, 127051, Moscow, Russia.
| | - Alexander Seliverstov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetnyi lane, 19, 127051, Moscow, Russia.
| | - Konstantin Gorbunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetnyi lane, 19, 127051, Moscow, Russia.
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17
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Walker JF, Jansen RK, Zanis MJ, Emery NC. Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. AMERICAN JOURNAL OF BOTANY 2015; 102:1751-2. [PMID: 26546126 DOI: 10.3732/ajb.1500299] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/29/2015] [Indexed: 05/02/2023]
Affiliation(s)
- Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA Biotechnology Research Group, Department of Biological Sciences, King Abdulaziz University, Jeddah 21589 Saudi Arabia
| | - Michael J Zanis
- Department of Biology, Seattle University, Seattle, Washington 98122 USA
| | - Nancy C Emery
- Department of Ecology & Evolutionary Biology, Campus Box 334, University of Colorado Boulder, Boulder, Colorado 80309-0334 USA
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18
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Abstract
Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial DNAs. However, much of the plastid-containing eukaryotic diversity falls outside of land plants, and the patterns of plastid DNA evolution for embryophytes do not necessarily reflect those of other groups. Recent analyses of plastid and mitochondrial substitution rates in diverse lineages have uncovered very different trends than those recorded for land plants. Here, I explore these new data and argue that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae. These findings have far-reaching implications for how we view plastid genomes and how their sequences are used for evolutionary analyses, and might ultimately reflect a general tendency toward more efficient DNA repair mechanisms in plastids than in mitochondria.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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19
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Kamikawa R, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biol Evol 2015; 7:1133-40. [PMID: 25840416 PMCID: PMC4419806 DOI: 10.1093/gbe/evv060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Unlike many other photosynthetic dinoflagellates, whose plastids contain a characteristic carotenoid peridinin, members of the genus Lepidodinium are the only known dinoflagellate species possessing green alga-derived plastids. However, the precise origin of Lepidodinium plastids has hitherto remained uncertain. In this study, we completely sequenced the plastid genome of Lepidodinium chlorophorum NIES-1868. Our phylogenetic analyses of 52 plastid-encoded proteins unite L. chlorophorum exclusively with a pedinophyte, Pedinomonas minor, indicating that the green-colored plastids in Lepidodinium spp. were derived from an endosymbiotic pedinophyte or a green alga closely related to pedinophytes. Our genome comparison incorporating the origin of the Lepidodinium plastids strongly suggests that the endosymbiont plastid genome acquired by the ancestral Lepidodinium species has lost genes encoding proteins involved in metabolism and biosynthesis, protein/metabolite transport, and plastid division during the endosymbiosis. We further discuss the commonalities and idiosyncrasies in genome evolution between the L. chlorophorum plastid and other plastids acquired through endosymbiosis of eukaryotic photoautotrophs.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Goro Tanifuji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Masanobu Kawachi
- The National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Hideaki Miyashita
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
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20
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Brembu T, Winge P, Tooming-Klunderud A, Nederbragt AJ, Jakobsen KS, Bones AM. The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer. Mar Genomics 2014; 16:17-27. [DOI: 10.1016/j.margen.2013.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/29/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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21
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Hovde BT, Starkenburg SR, Hunsperger HM, Mercer LD, Deodato CR, Jha RK, Chertkov O, Monnat RJ, Cattolico RA. The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. BMC Genomics 2014; 15:604. [PMID: 25034814 PMCID: PMC4226036 DOI: 10.1186/1471-2164-15-604] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation. RESULTS The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent 'CheY-like' two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes--algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs)--a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade. CONCLUSION The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.
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22
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Yang JB, Li DZ, Li HT. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour 2014; 14:1024-31. [PMID: 24620934 DOI: 10.1111/1755-0998.12251] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 11/30/2022]
Abstract
Chloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle-scale barcodes. Next-generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two major reasons for the paucity of completely sequenced chloroplast genomes: (i) massive amounts of fresh leaves are needed for chloroplast sequencing and (ii) there are considerable gaps in the sequenced chloroplast genomes of many plants because of the difficulty of isolating high-quality chloroplast DNA, preventing complete chloroplast genomes from being assembled. To overcome these obstacles, all known angiosperm chloroplast genomes available to date were analysed, and then we designed nine universal primer pairs corresponding to the highly conserved regions. Using these primers, angiosperm whole chloroplast genomes can be amplified using long-range PCR and sequenced using next-generation sequencing methods. The primers showed high universality, which was tested using 24 species representing major clades of angiosperms. To validate the functionality of the primers, eight species representing major groups of angiosperms, that is, early-diverging angiosperms, magnoliids, monocots, Saxifragales, fabids, malvids and asterids, were sequenced and assembled their complete chloroplast genomes. In our trials, only 100 mg of fresh leaves was used. The results show that the universal primer set provided an easy, effective and feasible approach for sequencing whole chloroplast genomes in angiosperms. The designed universal primer pairs provide a possibility to accelerate genome-scale data acquisition and will therefore magnify the phylogenetic resolution and species identification in angiosperms.
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Affiliation(s)
- Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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23
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Starkenburg SR, Kwon KJ, Jha RK, McKay C, Jacobs M, Chertkov O, Twary S, Rocap G, Cattolico RA. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics 2014; 15:212. [PMID: 24646409 PMCID: PMC3999925 DOI: 10.1186/1471-2164-15-212] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 03/11/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776. RESULTS The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome). CONCLUSIONS Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
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Affiliation(s)
- Shawn R Starkenburg
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Kyungyoon J Kwon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley 94720, CA, USA
| | - Ramesh K Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Cedar McKay
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
| | - Michael Jacobs
- Biology Department, University of Washington, Seattle 98195, WA, USA
| | - Olga Chertkov
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
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24
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Ruck EC, Nakov T, Jansen RK, Theriot EC, Alverson AJ. Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms. Genome Biol Evol 2014; 6:644-54. [PMID: 24567305 PMCID: PMC3971590 DOI: 10.1093/gbe/evu039] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 11/14/2022] Open
Abstract
Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.
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Affiliation(s)
| | - Teofil Nakov
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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25
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Dong W, Xu C, Cheng T, Lin K, Zhou S. Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of saxifragales. Genome Biol Evol 2013; 5:989-97. [PMID: 23595020 PMCID: PMC3673619 DOI: 10.1093/gbe/evt063] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Plastid genomes are an invaluable resource for plant biological studies. However, the number of completely sequenced plant plastid genomes is still small compared with the vast number of species. To provide an alternative generalized approach, we designed a set of 138 pairs of universal primers for amplifying (termed "short-range PCR") and sequencing the entire genomes of the angiosperm plastid genomes. The universality of the primers was tested by using species from the basal to asterid angiosperms. The polymerase chain reaction (PCR) success rate was higher than 96%. We sequenced the complete chloroplast genome of Liquidambar formosana as an example using this method and compared it to the genomes independently determined by long-range PCR (from 6.3 kb to 13.3 kb) and next-generation sequencing methods. The three genomes showed that they were completely identical. To test the phylogenetic efficiency of this method, we amplified and sequenced 18 chloroplast regions of 19 Saxifragales and Saxifragales-related taxa, as a case study, to reconstruct the phylogeny of all families of the order. Phylograms based on a combination of our data, together with those from GenBank, clearly indicate three family groups and three single families within the order. This set of universal primers is expected to accelerate the accumulation of angiosperm plastid genomes and to make faster mass data collection of plastid genomes for molecular systematics.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kui Lin
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- *Corresponding author: E-mail:
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26
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Wei L, Xin Y, Wang D, Jing X, Zhou Q, Su X, Jia J, Ning K, Chen F, Hu Q, Xu J. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. BMC Genomics 2013; 14:534. [PMID: 23915326 PMCID: PMC3750441 DOI: 10.1186/1471-2164-14-534] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/31/2013] [Indexed: 12/26/2022] Open
Abstract
Background Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes. Results Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species. Conclusion This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of microalgae was proposed which might be generally applicable to other microalgal genera and should serve as a valuable tool in the expanding algal biotechnology industry.
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Affiliation(s)
- Li Wei
- BioEnergy Genome Center and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
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27
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DePriest MS, Bhattacharya D, López-Bautista JM. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One 2013; 8:e68246. [PMID: 23894297 PMCID: PMC3716797 DOI: 10.1371/journal.pone.0068246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/26/2013] [Indexed: 11/20/2022] Open
Abstract
The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.
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Affiliation(s)
- Michael S DePriest
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America.
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28
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Wang X, Shao Z, Fu W, Yao J, Hu Q, Duan D. Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): its structural features and phylogenetic analyses with other photosynthetic plastids. Mar Genomics 2013; 10:1-9. [PMID: 23305622 DOI: 10.1016/j.margen.2012.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/19/2022]
Abstract
The chloroplast genome sequence of one brown seaweed, Saccharina japonica, was fully determined. It is characterized by 130,584 base pairs (bp) with a large and a small single-copy region (LSC and SSC), separated by two copies of inverted repeats (IR1 and IR2). The inverted repeat is 5015 bp long, and the sizes of SSC and LSC are 43,174 bp and 77,378 bp, respectively. The chloroplast genome of S. japonica consists of 139 protein-coding genes, 29 tRNA genes, and 3 ribosomal RNA genes. One intron was found in one tRNA-Leu gene in the chloroplast genome of S. japonica. Four types of overlapping genes were identified, ycf24 overlapped with ycf16 by 4 nucleotides (nt), ftrB overlapped with ycf12 by 6 nt, rpl4 and rpl23 overlapped by 8 nt, finally, psbC overlapped with psbD by 53 nt. With two sets of concatenated plastid protein data, 40-protein dataset and 26-protein dataset, the chloroplast phylogenetic relationship among S. japonica and the other photosynthetic species was evaluated. We found that the chloroplast genomes of haptophyte, cryptophyte and heterokont were not resolved into one cluster by the 40-protein dataset with amino acid composition bias, although it was recovered with strong support by the 26-protein dataset.
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Affiliation(s)
- Xiuliang Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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29
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Smith DR, Keeling PJ. Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids. J Eukaryot Microbiol 2012; 59:181-4. [PMID: 22236077 DOI: 10.1111/j.1550-7408.2011.00601.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 11/05/2011] [Indexed: 01/09/2023]
Abstract
Within plastid-bearing species, the relative rates of evolution between mitochondrial and plastid genomes are poorly studied, but for the few lineages in which they have been explored, including land plants and green algae, the mitochondrial DNA mutation rate is nearly always estimated to be lower than or equal to that of the plastid DNA. Here, we show that in protists from three distinct lineages with secondary, red algal-derived plastids, the opposite is true: their mitochondrial genomes are evolving 5-30 times faster than their plastid genomes, even when the plastid is nonphotosynthetic. These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode.
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Affiliation(s)
- David Roy Smith
- Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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30
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31
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Gao W, Shi X, Wu J, Jin Y, Zhang W, Meldrum DR. Phylogenetic and gene expression analysis of cyanobacteria and diatoms in the twilight waters of the temperate northeast Pacific Ocean. MICROBIAL ECOLOGY 2011; 62:765-775. [PMID: 21698402 DOI: 10.1007/s00248-011-9891-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/07/2011] [Indexed: 05/31/2023]
Abstract
In this study, to explore the microbial community structure and its functionality in the deep-sea environments, we initially performed a 16S ribosomal RNA (rRNA)-based community structure analyses for microbial communities in the sea water collected from sites of 765-790 m in depth in the Pacific Ocean. Interestingly, in the clone library we detected the presence of both photoautotrophic bacteria such as cyanobacteria and photoheterotrophic bacteria, such as Chloroflexus sp. To further explore the existence and diversity of possible light-utilizing microorganisms, we then constructed and analyzed a 23S rRNA plastid gene cloning library. The results showed that the majority of this cloning library was occupied by oxygenic photoautotrophic organisms, such as diatoms Thalassiosira spp. and cyanobacterium Synechococcus sp. In addition, the diversity of these oxygenic photoautotrophic organisms was very limited. Moreover, both reverse-transcription PCR and quantitative reverse-transcription PCR approaches had been employed to detect expression of the genes involved in protein synthesis and photosynthesis of photoautotrophic organisms, and the positive results were obtained. The possible mechanisms underlying the existence of very limited diversity of photosynthetic organisms at this depth of ocean, as well as the positive detection of rRNA and mRNA of diatom and cyanobacteria, were discussed.
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Affiliation(s)
- Weimin Gao
- Center for Biosignatures Discovery Automation, the Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA
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Green BR. Chloroplast genomes of photosynthetic eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:34-44. [PMID: 21443621 DOI: 10.1111/j.1365-313x.2011.04541.x] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplast genomes have retained a core set of genes from their cyanobacterial ancestor, most of them required for the light reactions of photosynthesis or functions connected with transcription and translation. Other genes have been transferred to the nucleus or were lost in a lineage-specific manner. The genomes are distinguished by the selection of genes retained, whether or not transcripts are edited, presence/absence of introns and small repeats and their physical organization. Plants and green algae have kept fewer plastid genes than either the red algae or the chromistan algae, which obtained their plastids from red algae by secondary endosymbiosis. Photosynthetic dinoflagellates have the fewest (fewer than 20), but still grow photoautotrophically. All chloroplast genomes map as a circle, but there have been extensive rearrangements of gene order even between related species. Genome sizes vary much more than gene content, depending on the extent of gene duplication and small repeats and the size of intergenic spacers.
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Affiliation(s)
- Beverley R Green
- Botany Department, University of British Columbia, #3529-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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Wu CS, Lin CP, Hsu CY, Wang RJ, Chaw SM. Comparative chloroplast genomes of pinaceae: insights into the mechanism of diversified genomic organizations. Genome Biol Evol 2011; 3:309-19. [PMID: 21402866 PMCID: PMC5654405 DOI: 10.1093/gbe/evr026] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pinaceae, the largest family of conifers, has diversified organizations of chloroplast genomes (cpDNAs) with the two typical inverted repeats (IRs) highly reduced. To unravel the mechanism of this genomic diversification, we examined the cpDNA organizations from 53 species of the ten Pinaceous genera, including those of Larix decidua (122,474 bp), Picea morrisonicola (124,168 bp), and Pseudotsuga wilsoniana (122,513 bp), which were firstly elucidated. The results uncovered four distinct cpDNA forms (A−C and P) that are due to rearrangements of two ∼20 and ∼21 kb specific fragments. The C form was documented for the first time and the A form might be the most ancestral one. In addition, only the individuals of Ps. macrocarpa and Ps. wilsoniana were detected to have isomeric cpDNA forms. Three types (types 1−3) of Pinaceae-specific repeats situated nearby the rearranged fragments were found to be syntenic. We hypothesize that type 1 (949 ± 343 bp) and type 3 (608 ± 73 bp) repeats are substrates for homologous recombination (HR), whereas type 2 repeats are likely inactive for HR because of their relatively short sizes (151 ± 30 bp). Conversions among the four distinct forms may be achieved by HR and mediated by type 1 or 3 repeats, thus resulting in increased diversity of cpDNA organizations. We propose that in the Pinaceae cpDNAs, the reduced IRs have lost HR activity, then decreasing the diversity of cpDNA organizations, but the specific repeats that the evolution endowed Pinaceae complement the reduced IRs and increase the diversity of cpDNA organizations.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Lommer M, Roy AS, Schilhabel M, Schreiber S, Rosenstiel P, LaRoche J. Recent transfer of an iron-regulated gene from the plastid to the nuclear genome in an oceanic diatom adapted to chronic iron limitation. BMC Genomics 2010; 11:718. [PMID: 21171997 PMCID: PMC3022921 DOI: 10.1186/1471-2164-11-718] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 12/20/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environments. Compared to its coastal relative Thalassiosira pseudonana, the oceanic diatom Thalassiosira oceanica is highly tolerant to iron limitation. The adaptation to low-iron conditions in T. oceanica has been attributed to a decrease in the photosynthetic components that are rich in iron. Genomic information on T. oceanica may shed light on the genetic basis of the physiological differences between the two species. RESULTS The complete 141790 bp sequence of the T. oceanica chloroplast genome [GenBank: GU323224], assembled from massively parallel pyrosequencing (454) shotgun reads, revealed that the petF gene encoding for ferredoxin, which is localized in the chloroplast genome in T. pseudonana and other diatoms, has been transferred to the nucleus in T. oceanica. The iron-sulfur protein ferredoxin, a key element of the chloroplast electron transport chain, can be replaced by the iron-free flavodoxin under iron-limited growth conditions thereby contributing to a reduction in the cellular iron requirements. From a comparison to the genomic context of the T. pseudonana petF gene, the T. oceanica ortholog can be traced back to its chloroplast origin. The coding potential of the T. oceanica chloroplast genome is comparable to that of T. pseudonana and Phaeodactylum tricornutum, though a novel expressed ORF appears in the genomic region that has been subjected to rearrangements linked to the petF gene transfer event. CONCLUSIONS The transfer of the petF from the cp to the nuclear genome in T. oceanica represents a major difference between the two closely related species. The ability of T. oceanica to tolerate iron limitation suggests that the transfer of petF from the chloroplast to the nuclear genome might have contributed to the ecological success of this species.
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Affiliation(s)
- Markus Lommer
- Leibniz Institute of Marine Sciences at Kiel University IFM-GEOMAR, Kiel, Germany
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Jiroutová K, Kořený L, Bowler C, Oborník M. A gene in the process of endosymbiotic transfer. PLoS One 2010; 5:e13234. [PMID: 20949086 PMCID: PMC2950852 DOI: 10.1371/journal.pone.0013234] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 09/13/2010] [Indexed: 12/02/2022] Open
Abstract
Background The endosymbiotic birth of organelles is accompanied by massive transfer of endosymbiont genes to the eukaryotic host nucleus. In the centric diatom Thalassiosira pseudonana the Psb28 protein is encoded in the plastid genome while a second version is nuclear-encoded and possesses a bipartite N-terminal presequence necessary to target the protein into the diatom complex plastid. Thus it can represent a gene captured during endosymbiotic gene transfer. Methodology/Principal Findings To specify the origin of nuclear- and plastid-encoded Psb28 in T. pseudonana we have performed extensive phylogenetic analyses of both mentioned genes. We have also experimentally tested the intracellular location of the nuclear-encoded Psb28 protein (nuPsb28) through transformation of the diatom Phaeodactylum tricornutum with the gene in question fused to EYFP. Conclusions/Significance We show here that both versions of the psb28 gene in T. pseudonana are transcribed. We also provide experimental evidence for successful targeting of the nuPsb28 fused with EYFP to the diatom complex plastid. Extensive phylogenetic analyses demonstrate that nucleotide composition of the analyzed genes deeply influences the tree topology and that appropriate methods designed to deal with a compositional bias of the sequences and the long branch attraction artefact (LBA) need to be used to overcome this obstacle. We propose that nuclear psb28 in T. pseudonana is a duplicate of a plastid localized version, and that it has been transferred from its endosymbiont.
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Affiliation(s)
- Kateřina Jiroutová
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Luděk Kořený
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, Ecole Normale Supérieure, Paris, France
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
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Imanian B, Pombert JF, Keeling PJ. The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS One 2010; 5:e10711. [PMID: 20502706 PMCID: PMC2873285 DOI: 10.1371/journal.pone.0010711] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/23/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In one small group of dinoflagellates, photosynthesis is carried out by a tertiary endosymbiont derived from a diatom, giving rise to a complex cell that we collectively refer to as a 'dinotom'. The endosymbiont is separated from its host by a single membrane and retains plastids, mitochondria, a large nucleus, and many other eukaryotic organelles and structures, a level of complexity suggesting an early stage of integration. Although the evolution of these endosymbionts has attracted considerable interest, the plastid genome has not been examined in detail, and indeed no tertiary plastid genome has yet been sequenced. METHODOLOGY/PRINCIPAL FINDINGS Here we describe the complete plastid genomes of two closely related dinotoms, Durinskia baltica and Kryptoperidinium foliaceum. The D. baltica (116470 bp) and K. foliaceum (140426 bp) plastid genomes map as circular molecules featuring two large inverted repeats that separate distinct single copy regions. The organization and gene content of the D. baltica plastid closely resemble those of the pennate diatom Phaeodactylum tricornutum. The K. foliaceum plastid genome is much larger, has undergone more reorganization, and encodes a putative tyrosine recombinase (tyrC) also found in the plastid genome of the heterokont Heterosigma akashiwo, and two putative serine recombinases (serC1 and serC2) homologous to recombinases encoded by plasmids pCf1 and pCf2 in another pennate diatom, Cylindrotheca fusiformis. The K. foliaceum plastid genome also contains an additional copy of serC1, two degenerate copies of another plasmid-encoded ORF, and two non-coding regions whose sequences closely resemble portions of the pCf1 and pCf2 plasmids. CONCLUSIONS/SIGNIFICANCE These results suggest that while the plastid genomes of two dinotoms share very similar gene content and genome organization with that of the free-living pennate diatom P. tricornutum, the K. folicaeum plastid genome has absorbed two exogenous plasmids. Whether this took place before or after the tertiary endosymbiosis is not clear.
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Affiliation(s)
- Behzad Imanian
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-François Pombert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Le Corguillé G, Pearson G, Valente M, Viegas C, Gschloessl B, Corre E, Bailly X, Peters AF, Jubin C, Vacherie B, Cock JM, Leblanc C. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids. BMC Evol Biol 2009; 9:253. [PMID: 19835607 PMCID: PMC2765969 DOI: 10.1186/1471-2148-9-253] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 10/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heterokont algae, together with cryptophytes, haptophytes and some alveolates, possess red-algal derived plastids. The chromalveolate hypothesis proposes that the red-algal derived plastids of all four groups have a monophyletic origin resulting from a single secondary endosymbiotic event. However, due to incongruence between nuclear and plastid phylogenies, this controversial hypothesis remains under debate. Large-scale genomic analyses have shown to be a powerful tool for phylogenetic reconstruction but insufficient sequence data have been available for red-algal derived plastid genomes. RESULTS The chloroplast genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus, have been fully sequenced. These species represent two distinct orders of the Phaeophyceae, which is a major group within the heterokont lineage. The sizes of the circular plastid genomes are 139,954 and 124,986 base pairs, respectively, the size difference being due principally to the presence of longer inverted repeat and intergenic regions in E. siliculosus. Gene contents of the two plastids are similar with 139-148 protein-coding genes, 28-31 tRNA genes, and 3 ribosomal RNA genes. The two genomes also exhibit very similar rearrangements compared to other sequenced plastid genomes. The tRNA-Leu gene of E. siliculosus lacks an intron, in contrast to the F. vesiculosus and other heterokont plastid homologues, suggesting its recent loss in the Ectocarpales. Most of the brown algal plastid genes are shared with other red-algal derived plastid genomes, but a few are absent from raphidophyte or diatom plastid genomes. One of these regions is most similar to an apicomplexan nuclear sequence. The phylogenetic relationship between heterokonts, cryptophytes and haptophytes (collectively referred to as chromists) plastids was investigated using several datasets of concatenated proteins from two cyanobacterial genomes and 18 plastid genomes, including most of the available red algal and chromist plastid genomes. CONCLUSION The phylogenetic studies using concatenated plastid proteins still do not resolve the question of the monophyly of all chromist plastids. However, these results support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies.
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Affiliation(s)
- Gildas Le Corguillé
- CNRS, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
| | - Gareth Pearson
- Centre of Marine Sciences, University of Algarve, Marine Ecology and Evolution, Faro, Portugal
| | - Marta Valente
- Centre of Marine Sciences, University of Algarve, Marine Ecology and Evolution, Faro, Portugal
| | - Carla Viegas
- Centre of Marine Sciences, University of Algarve, Marine Ecology and Evolution, Faro, Portugal
| | - Bernhard Gschloessl
- CNRS, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
| | - Erwan Corre
- CNRS, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
| | - Xavier Bailly
- CNRS, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, FR2424, Computer and Genomics Resource Centre, Station Biologique, Roscoff, France
| | - Akira F Peters
- CNRS, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
| | - Claire Jubin
- CEA, DSV, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | | | - J Mark Cock
- CNRS, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
| | - Catherine Leblanc
- CNRS, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
- UPMC Univ. Paris 06, UMR7139, Marine Plants and Biomolecules, Station Biologique, Roscoff, France
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Turmel M, Gagnon MC, O'Kelly CJ, Otis C, Lemieux C. The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol Biol Evol 2008; 26:631-48. [PMID: 19074760 DOI: 10.1093/molbev/msn285] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of chlorophytes and the reduction of cell size in some lineages. Seven prasinophyte lineages, four of which exhibit a coccoid cell organization (no flagella nor scales), were uncovered from analysis of nuclear-encoded 18S rDNA data; however, their order of divergence remains unknown. In this study, the chloroplast genome sequences of the scaly quadriflagellate Pyramimonas parkeae (clade I), the coccoid Pycnococcus provasolii (clade V), and the scaly uniflagellate Monomastix (unknown affiliation) were determined, annotated, and compared with those previously reported for green algae/land plants, including two prasinophytes (Nephroselmis olivacea, clade III and Ostreococcus tauri, clade II). The chlorarachniophyte Bigelowiella natans and the euglenid Euglena gracilis, whose chloroplasts originate presumably from distinct green algal endosymbionts, were also included in our comparisons. The three newly sequenced prasinophyte genomes differ considerably from one another and from their homologs in overall structure, gene content, and gene order, with the 80,211-bp Pycnococcus and 114,528-bp Monomastix genomes (98 and 94 conserved genes, respectively) resembling the 71,666-bp Ostreococcus genome (88 genes) in featuring a significantly reduced gene content. The 101,605-bp Pyramimonas genome (110 genes) features two conserved genes (rpl22 and ycf65) and ancestral gene linkages previously unrecognized in chlorophytes as well as a DNA primase gene putatively acquired from a virus. The Pyramimonas and Euglena cpDNAs revealed uniquely shared derived gene clusters. Besides providing unequivocal evidence that the green algal ancestor of the euglenid chloroplasts belonged to the Pyramimonadales, phylogenetic analyses of concatenated chloroplast genes and proteins elucidated the position of Monomastix and showed that the Mamiellales, a clade comprising Ostreococcus and Monomastix, are sister to the Pyramimonadales + Euglena clade. Our results also revealed that major reduction in gene content and restructuring of the chloroplast genome occurred in conjunction with important changes in cell organization in at least two independent prasinophyte lineages, the Mamiellales and the Pycnococcaceae.
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Affiliation(s)
- Monique Turmel
- Département de Biochimie et de Microbiologie, Université Laval, Québec (Québec), Canada.
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Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc Natl Acad Sci U S A 2008; 105:17867-71. [PMID: 19004808 DOI: 10.1073/pnas.0804968105] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3' flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty ("green animals") and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.
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