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San MH, Kawamura Y, Kimura K, Witharana EP, Shimogiri T, Aye SS, Min TT, Aung C, Khaing MM, Nagano Y. Characterization and organelle genome sequencing of Pyropia species from Myanmar. Sci Rep 2023; 13:15677. [PMID: 37735516 PMCID: PMC10514050 DOI: 10.1038/s41598-023-42262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions.
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Affiliation(s)
- Myat Htoo San
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
| | | | - Kei Kimura
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | | | - Thu Thu Min
- Marine Science Department, Pathein University, Pathein, Myanmar
| | - Cherry Aung
- Marine Science Department, Myeik University, Myeik, Myanmar
| | | | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
- Graduate School of Advanced Health Science, Saga University, Saga, Japan.
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Mikami K, Khoa HV. Membrane Fluidization Governs the Coordinated Heat-Inducible Expression of Nucleus- and Plastid Genome-Encoded Heat Shock Protein 70 Genes in the Marine Red Alga Neopyropia yezoensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112070. [PMID: 37299052 DOI: 10.3390/plants12112070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Heat shock protein 70 (HSP70) is an evolutionarily conserved protein chaperone in prokaryotic and eukaryotic organisms. This family is involved in the maintenance of physiological homeostasis by ensuring the proper folding and refolding of proteins. The HSP70 family in terrestrial plants can be divided into cytoplasm, endoplasmic reticulum (ER)-, mitochondrion (MT)-, and chloroplast (CP)-localized HSP70 subfamilies. In the marine red alga Neopyropia yezoensis, the heat-inducible expression of two cytoplasmic HSP70 genes has been characterized; however, little is known about the presence of other HSP70 subfamilies and their expression profiles under heat stress conditions. Here, we identified genes encoding one MT and two ER HSP70 proteins and confirmed their heat-inducible expression at 25 °C. In addition, we determined that membrane fluidization directs gene expression for the ER-, MT-, and CP-localized HSP70 proteins as with cytoplasmic HSP70s. The gene for the CP-localized HSP70 is carried by the chloroplast genome; thus, our results indicate that membrane fluidization is a trigger for the coordinated heat-driven induction of HSP70 genes harbored by the nuclear and plastid genomes in N. yezoensis. We propose this mechanism as a unique regulatory system common in the Bangiales, in which the CP-localized HSP70 is usually encoded in the chloroplast genome.
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Affiliation(s)
- Koji Mikami
- School of Food Industrial Sciences, Miyagi University, Hatatate 2-2-1, Sendai 982-0215, Japan
| | - Ho Viet Khoa
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-Cho, Hakodate 041-8611, Japan
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Zhang Z, Wang J, Zhang X, Guan X, Gao T, Mao Y, Poetsch A, Wang D. ChIP-Based Nuclear DNA Isolation for Genome Sequencing in Pyropia to Remove Cytosol and Bacterial DNA Contamination. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091883. [PMID: 37176941 PMCID: PMC10181236 DOI: 10.3390/plants12091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023]
Abstract
Contamination from cytosolic DNA (plastid and mitochondrion) and epiphytic bacteria is challenging the efficiency and accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is closely associated with histone proteins. In this study, we applied Chromatin Immunoprecipitation (ChIP) of histone H3 to isolate nuclear DNA, followed by high-throughput sequencing. More than 99.41% of ChIP-sequencing data were successfully aligned to the reference nuclear genome; this was remarkably higher than those from direct extraction and direct extraction data, in which 40.96% to 42.95% are from plastids. The proportion of data that were mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP data can cover up to 89.00% of the nuclear genome, higher than direct extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in the ChIP extraction method. This ChIP extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in a genome resequencing project and providing strictly purified reference data for genome assembly. The method's applicability to other macroalgae makes it a valuable contribution to the algal research community.
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Affiliation(s)
- Zehao Zhang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
| | - Junhao Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
| | - Xiaoqian Zhang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
| | - Xiaowei Guan
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
| | - Tian Gao
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572000, China
| | - Ansgar Poetsch
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- Department of Plant Biochemistry, Ruhr University Bochum, 44787 Bochum, Germany
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266000, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
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Mikami K, Takahashi M. Life cycle and reproduction dynamics of Bangiales in response to environmental stresses. Semin Cell Dev Biol 2023; 134:14-26. [PMID: 35428563 DOI: 10.1016/j.semcdb.2022.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/16/2022]
Abstract
Red algae of the order Bangiales are notable for exhibiting flexible promotion of sexual and asexual reproductive processes by environmental stresses. This flexibility indicates that a trade-off between vegetative growth and reproduction occurs in response to environmental stresses that influence the timing of phase transition within the life cycle. Despite their high phylogenetic divergence, both filamentous and foliose red alga in the order Bangiales exhibit a haploid-diploid life cycle, with a haploid leafy or filamentous gametophyte (thallus) and a diploid filamentous sporophyte (conchocelis). Unlike haploid-diploid life cycles in other orders, the gametophyte in Bangiales is generated independently of meiosis; the regulation of this generation transition is not fully understood. Based on transcriptome and gene expression analyses, the originally proposed biphasic model for alternation of generations in Bangiales was recently updated to include a third stage. Along with the haploid gametophyte and diploid sporophyte, the triphasic framework recognizes a diploid conchosporophyte-a conchosporangium generated on the conchocelis-phase and previously considered to be part of the sporophyte. In addition to this sexual life cycle, some Bangiales species have an asexual life cycle in which vegetative cells of the thallus develop into haploid asexual spores, which are then released from the thallus to produce clonal thalli. Here, we summarize the current knowledge of the triphasic life cycle and life cycle trade-off in Neopyropia yezoensis and 'Bangia' sp. as model organisms for the Bangiales.
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Affiliation(s)
- Koji Mikami
- Department of Integrative Studies of Plant and Animal Production, School of Food Industrial Sciences, Miyagi University, Sendai, Japan.
| | - Megumu Takahashi
- Department of Ocean and Fisheries Sciences, Faculty of Bio-Industry, Tokyo University of Agriculture, Abashiri, Japan
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Park SH, Kyndt JA, Brown JK. Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer. Life (Basel) 2022; 12:life12030458. [PMID: 35330209 PMCID: PMC8955559 DOI: 10.3390/life12030458] [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: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.
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Affiliation(s)
- Sang-Hyuck Park
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; (S.-H.P.); (J.K.B.)
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO 81001, USA
| | - John A. Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
- Correspondence:
| | - Judith K. Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; (S.-H.P.); (J.K.B.)
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Genomic diversity of 39 samples of Pyropia species grown in Japan. PLoS One 2021; 16:e0252207. [PMID: 34106965 PMCID: PMC8189503 DOI: 10.1371/journal.pone.0252207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.
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Li R, Jia X, Zhang J, Jia S, Liu T, Qu J, Wang X. The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:747036. [PMID: 34804089 PMCID: PMC8602799 DOI: 10.3389/fpls.2021.747036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/04/2021] [Indexed: 05/03/2023]
Abstract
Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.
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Affiliation(s)
- Ruoran Li
- College of Life Sciences, Yantai University, Yantai, China
| | - Xuli Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Shangang Jia,
| | - Tao Liu
- College of Life Sciences, Yantai University, Yantai, China
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Tao Liu,
| | - Jiangyong Qu
- College of Life Sciences, Yantai University, Yantai, China
- Jiangyong Qu,
| | - Xumin Wang
- College of Life Sciences, Yantai University, Yantai, China
- Xumin Wang,
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Cho TJ, Rhee MS. Health Functionality and Quality Control of Laver ( Porphyra, Pyropia): Current Issues and Future Perspectives as an Edible Seaweed. Mar Drugs 2019; 18:E14. [PMID: 31877971 PMCID: PMC7024182 DOI: 10.3390/md18010014] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
The growing interest in laver as a food product and as a source of substances beneficial to health has led to global consumer demand for laver produced in a limited area of northeastern Asia. Here we review research into the benefits of laver consumption and discuss future perspectives on the improvement of laver product quality. Variation in nutritional/functional values among product types (raw and processed (dried, roasted, or seasoned) laver) makes product-specific nutritional analysis a prerequisite for accurate prediction of health benefits. The effects of drying, roasting, and seasoning on the contents of both beneficial and harmful substances highlight the importance of managing laver processing conditions. Most research into health benefits has focused on substances present at high concentrations in laver (porphyran, Vitamin B12, taurine), with assessment of the expected effects of laver consumption. Mitigation of chemical/microbiological risks and the adoption of novel technologies to exploit under-reported biochemical characteristics of lavers are suggested as key strategies for the further improvement of laver product quality. Comprehensive analysis of the literature regarding laver as a food product and as a source of biomedical compounds highlights the possibilities and challenges for application of laver products.
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Affiliation(s)
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Korea;
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Petersen G, Darby H, Lam VKY, Pedersen HÆ, Merckx VSFT, Zervas A, Seberg O, Graham SW. Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes. ANNALS OF BOTANY 2019; 124:791-807. [PMID: 31346602 PMCID: PMC6868387 DOI: 10.1093/aob/mcz114] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/24/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis. METHODS We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives. KEY RESULTS Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes. CONCLUSIONS Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.
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Affiliation(s)
- G Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- For correspondence. E-mail:
| | - H Darby
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - V K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - H Æ Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - A Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Denmark
| | - O Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
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A Simple Procedure to Observe Phototropic Responses in the Red Seaweed Pyropia yezoensis. Methods Mol Biol 2019. [PMID: 30694470 DOI: 10.1007/978-1-4939-9015-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The marine red seaweed Pyropia yezoensis exhibits phototropic responses in gametophyte and conchosporangia phases, but not in sporophytes. These responses are easily monitored with a simple culturing box that has one side open to allow for unilateral light irradiation within an incubator. Confirmation of phototropic responses is achieved by changing the direction of unilateral light irradiation via rotation of the culture dishes clockwise 90°.
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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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Kitade Y, Miyabe Y, Yamamoto Y, Takeda H, Shimizu T, Yasui H, Kishimura H. Structural characteristics of phycobiliproteins from red alga Mazzaella japonica. J Food Biochem 2017. [DOI: 10.1111/jfbc.12436] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yumi Kitade
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Yoshikatsu Miyabe
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Yohei Yamamoto
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Hirohumi Takeda
- Fisheries Research Department, Hokkaido Research Organization, Abashiri Fishries; Research Institute; Hokkaido Japan
| | - Takeshi Shimizu
- Department of Research and Development; Hokkaido Industrial Technology Center; Hakodate Hokkaido Japan
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
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Carvalho EL, Wallau GL, Rangel DL, Machado LC, Pereira AB, Victoria FDC, Boldo JT, Pinto PM. Phylogenetic positioning of the Antarctic alga Prasiola crispa (Trebouxiophyceae) using organellar genomes and their structural analysis. JOURNAL OF PHYCOLOGY 2017; 53:908-915. [PMID: 28394430 DOI: 10.1111/jpy.12541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/09/2017] [Indexed: 06/07/2023]
Abstract
Antarctica is one of the most difficult habitats for sustaining life on earth; organisms that live there have developed different strategies for survival. Among these organisms is the green alga Prasiola crispa, belonging to the class Trebouxiophyceae. The literature on P. crispa taxonomy is scarce, and many gaps in the evolutionary relationship with its closest relatives remain. The goal of this study was to analyze the evolutionary relationships between P. crispa and other green algae using plastid and mitochondrial genomes. In addition, we analyzed the synteny conservation of these genomes of P. crispa with those of closely related species. Based on the plastid genome, P. crispa grouped with Prasiolopsis sp. SAG 84.81, another Trebouxiophyceaen species from the Prasiola clade. Based on the mitochondrial genome analysis, P. crispa grouped with other Trebouxiophyceaen species but had a basal position. The structure of the P. crispa chloroplast genome had low synteny with Prasiolopsis sp. SAG 84.81, despite some conserved gene blocks. The same was observed in the mitochondrial genome compared with Coccomyxa subellipsoidea C-169. We were able to establish the phylogenetic position of P. crispa with other species of Trebouxiophyceae using its genomes. In addition, we described the plasticity of these genomes using a structural analysis. The plastid and mitochondrial genomes of P. crispa will be useful for further genetic studies, phylogenetic analysis and resource protection of P. crispa as well as for further phylogenetic analysis of Trebouxiophyceaen green algae.
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Affiliation(s)
- Evelise Leis Carvalho
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia Centro de Pesquisas Aggeu Magalhães, Fiocruz, Recife, 50740-465, Brazil
| | - Darlene Lopes Rangel
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Laís Ceschini Machado
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | | | | | | | - Paulo Marcos Pinto
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
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Nan F, Feng J, Lv J, Liu Q, Fang K, Gong C, Xie S. Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence. Sci Rep 2017; 7:2934. [PMID: 28592899 PMCID: PMC5462760 DOI: 10.1038/s41598-017-03235-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/25/2017] [Indexed: 01/30/2023] Open
Abstract
Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415–484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.
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Affiliation(s)
- Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Kunpeng Fang
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Chaoyan Gong
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, (030006), China.
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15
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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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16
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Kong F, Zhao H, Liu W, Li N, Mao Y. Construction of Plastid Expression Vector and Development of Genetic Transformation System for the Seaweed Pyropia yezoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:147-156. [PMID: 28233074 DOI: 10.1007/s10126-017-9736-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
Pyropia yezoensis, belonging to the Rhodophyta, is an economically important seaweed. In this study, we developed a high-efficiency plastid transformation platform for P. yezoensis. In the plastid transformation vector, psbA UTR of P. yezoensis, including the promoter and 3' UTR, was used to express foreign genes. The integration site was a transcriptionally active intergenic region between the rrsB and trnI genes, located in the inverted repeat regions of the plastid genome. The CAT and eGFP genes were integrated into the plastid genome at this site. The expression of CAT in the transformants confers resistance to chloramphenicol through the action of chloramphenicol acetyltransferase, which inactivates the drug, thereby allowing the plant to grow well under selective pressure. The eGFP fluorescence signal was also observed in transformed cells and the transformants. The average survival rate of treated cells was estimated to be approximately 4.2‰ (4 transplastomic colonies per 1000 gametophyte cells). Multiple-PCR analyses confirmed that the CAT and eGFP genes were successfully integrated in the site between rrsB and trnI. Western blot also showed eGFP expression in the cells of transformants. Thus, this study presents the first convenient plastid gene expression system for P. yezoensis and provides an important platform for studying gene function in P. yezoensis.
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Affiliation(s)
- Fanna Kong
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Hailong Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Weixun Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Na Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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17
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Ng PK, Lin SM, Lim PE, Liu LC, Chen CM, Pai TW. Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae. BMC Genomics 2017; 18:40. [PMID: 28061748 PMCID: PMC5217408 DOI: 10.1186/s12864-016-3453-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined. RESULTS The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support. CONCLUSIONS Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.
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Affiliation(s)
- Poh-Kheng Ng
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Li-Chia Liu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Chien-Ming Chen
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244 Taiwan
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18
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Isolation of Plastid Ribosomes. Methods Mol Biol 2016. [PMID: 27730617 DOI: 10.1007/978-1-4939-6533-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Plastid ribosomes are responsible for a large part of the protein synthesis in plant leaves, green algal cells, and the vast majority in the thalli of red algae. Plastid translation is necessary not only for photosynthesis but also for development/differentiation of plants and algae. While some isolated plastid ribosomes from a few green lineages have been characterized by biochemical and proteomic approaches, in-depth proteomics including analyses of posttranslational modifications and processing, comparative proteomics of plastid ribosomes isolated from the cells grown under different conditions, and those from different taxa are still to be carried out. Establishment of isolation methods for pure plastid ribosomes from a wider range of species would be beneficial to study the relationship between structure, function, and evolution of plastid ribosomes. Here I describe methodologies and provide example protocols for extraction and isolation of plastid ribosomes from a unicellular green alga (Chlamydomonas reinhardtii), a land plant (Arabidopsis thaliana), and a marine red macroalga (Pyropia yezoensis).
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19
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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: 55] [Impact Index Per Article: 6.9] [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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20
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Miyabe Y, Furuta T, Takeda T, Kanno G, Shimizu T, Tanaka Y, Gai Z, Yasui H, Kishimura H. Structural Properties of Phycoerythrin from DulsePalmaria palmata. J Food Biochem 2016. [DOI: 10.1111/jfbc.12301] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoshikatsu Miyabe
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Tomoe Furuta
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Tomoyuki Takeda
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Gaku Kanno
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Takeshi Shimizu
- Department of Research and Development; Hokkaido Industrial Technology Center; Hakodate Hokkaido 041-0801 Japan
| | - Yoshikazu Tanaka
- Laboratory of X-Ray Structural Biology, Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
- Japan Science and Technology Agency, PRESTO; Sapporo 060-0810 Japan
| | - Zuoqi Gai
- Laboratory of X-Ray Structural Biology, Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido 041-8611 Japan
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21
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Du Q, Bi G, Mao Y, Sui Z. The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae. JOURNAL OF PHYCOLOGY 2016; 52:441-50. [PMID: 27273536 DOI: 10.1111/jpy.12406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/19/2016] [Indexed: 05/27/2023]
Abstract
The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein-coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya).
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Affiliation(s)
- Qingwei Du
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guiqi Bi
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
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22
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Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci Rep 2016; 6:23744. [PMID: 27030297 PMCID: PMC4814812 DOI: 10.1038/srep23744] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, 325-902, Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Korea
| | - Kathy Ann Miller
- Herbarium, University of California at Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, California, 94720-2465, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
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Takahashi M, Mikami K. Phototropism in the Marine Red Macroalga <i>Pyropia yezoensis</i>. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/ajps.2016.717211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Wang L, Mao Y, Kong F, Cao M, Sun P. Genome-wide expression profiles of Pyropia haitanensis in response to osmotic stress by using deep sequencing technology. BMC Genomics 2015; 16:1012. [PMID: 26611675 PMCID: PMC4661969 DOI: 10.1186/s12864-015-2226-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 11/17/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Pyropia haitanensis is an economically important marine crop grown in harsh intertidal habitats of southern China; it is also an excellent model system for studying mechanisms of stress tolerance. To understand the molecular mechanisms underlying osmotic tolerance and adaptation to intertidal environments, a comprehensive analysis of genome-wide gene expression profiles in response to dehydration and rehydration in Py. haitanensis was undertaken using digital gene expression profile (DGE) approaches combined with de novo transcriptome sequencing. RESULTS RNA-sequencing of the pooled RNA samples from different developmental phases and stress treatments was performed, which generated a total of 47.7 million clean reads. These reads were de novo assembled into 28,536 unigenes (≥ 200 bp), of which 18,217 unigenes (63.83 %) were annotated in at least one reference database. DGE analysis was performed on four treatments (two biological replicates per treatment), which included moderate dehydration, severe dehydration, rehydration, and normal conditions. The number of raw reads per sample ranged from 12.47 to 15.79 million, with an average of 14.69 million reads per sample. After quality filtering, the number of clean reads per sample ranged from 11.83 to 15.04 million. All distinct sequencing reads were annotated using the transcriptome of Py. haitanensis as reference. A total of 1,681 unigenes showed significant differential expression between moderate dehydration and normal conditions, in which 977 genes were upregulated, and 704 genes were downregulated. Between severe dehydration and normal conditions, 1,993 unigenes showed significantly altered expression, which included both upregulated (1,219) and downregulated genes (774). In addition, 1,086 differentially expressed genes were detected between rehydration and normal conditions, of which 720 genes were upregulated and 366 unigenes were downregulated. Most gene expression patterns in response to dehydration differed from that of rehydration, except for the synthesis of unsaturated fatty acids, several transcription factor families, and molecular chaperones that have been collectively implicated in the processes of dehydration and rehydration in Py. haitanensis. CONCLUSIONS Taken together, these data provide a global high-resolution analysis of gene expression changes during osmotic stress that could potentially serve as a key resource for understanding the biology of osmotic acclimation in intertidal red seaweed.
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Affiliation(s)
- Li Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
- Institute of Plant Resources, Dalian Nationalities University, Dalian, 116600, China.
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
| | - Min Cao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
| | - Peipei Sun
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
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25
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Zhang L, Wang X, Liu T, Wang H, Wang G, Chi S, Liu C. Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae). PLoS One 2015; 10:e0140144. [PMID: 26444909 PMCID: PMC4596871 DOI: 10.1371/journal.pone.0140144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/21/2015] [Indexed: 11/19/2022] Open
Abstract
Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes.
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Affiliation(s)
- Lei Zhang
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Tao Liu
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Haiyang Wang
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Shan Chi
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Cui Liu
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
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Zhang L, Wang X, Liu T, Wang G, Chi S, Liu C, Wang H. Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. PLoS One 2015; 10:e0139366. [PMID: 26426800 PMCID: PMC4591262 DOI: 10.1371/journal.pone.0139366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/10/2015] [Indexed: 01/13/2023] Open
Abstract
In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.
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Affiliation(s)
- Lei Zhang
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Tao Liu
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Shan Chi
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Cui Liu
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
| | - Haiyang Wang
- Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People’s Republic of China
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Cao M, Yuan XL, Bi G. Complete sequence and analysis of plastid genomes of Pseudo-nitzschia multiseries (Bacillariophyta). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2897-8. [DOI: 10.3109/19401736.2015.1060428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Min Cao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Long Yuan
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Guiqi Bi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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28
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Reyes-Prieto A. The basic genetic toolkit to move in with your photosynthetic partner. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Harden LK, Morales KM, Hughey JR. Identification of a new marine algal species Pyropia nitida sp. nov. (Bangiales: Rhodophyta) from Monterey, California. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3058-62. [PMID: 26153737 DOI: 10.3109/19401736.2015.1063137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
An unidentified marine red algal species classified in Pyropia J. Agardh was discovered from Monterey, CA. Morphological, barcode, and complete mitochondrial genome analysis of the alga support its recognition as a new species, Pyropia nitida sp. nov. The species is a high-intertidal, winter annual that is lanceolate in shape, monostromatic, and dioecious. Based on CO1 sequences, P. nitida is closely allied with the P. nereocystis clade. The mitogenome of P. nitida is 35 313 bp in length and contains 53 genes, including two ribosomal RNAs, 24 transfer RNAs, four ribosomal proteins, two ymfs, four ORFs, and 17 genes involved in electron transport and oxidative phosphorylation. The results support the recognition of P. nitida as distinct from the morphologically similar P. lanceolata.
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Affiliation(s)
- Leeanne K Harden
- a Division of Mathematics , Science, and Engineering, Hartnell College , Salinas , CA , USA
| | - Karina M Morales
- a Division of Mathematics , Science, and Engineering, Hartnell College , Salinas , CA , USA
| | - Jeffery R Hughey
- a Division of Mathematics , Science, and Engineering, Hartnell College , Salinas , CA , USA
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A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene. BIOMED RESEARCH INTERNATIONAL 2015; 2015:510598. [PMID: 26114108 PMCID: PMC4465662 DOI: 10.1155/2015/510598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/29/2014] [Accepted: 09/13/2014] [Indexed: 11/23/2022]
Abstract
We report the database of plastid protein families from red algae, secondary and tertiary rhodophyte-derived plastids, and Apicomplexa constructed with the novel method to infer orthology. The families contain proteins with maximal sequence similarity and minimal paralogous content. The database contains 6509 protein entries, 513 families and 278 nonsingletons (from which 230 are paralog-free, and among the remaining 48, 46 contain at maximum two proteins per species, and 2 contain at maximum three proteins per species). The method is compared with other approaches. Expression regulation of the moeB gene is studied using this database and the model of RNA polymerase competition. An analogous database obtained for green algae and their symbiotic descendants, and applications based on it are published earlier.
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Lai XJ, Yang R, Luo QJ, Chen JJ, Chen HM, Yan XJ. Glycerol-3-phosphate metabolism plays a role in stress response in the red alga Pyropia haitanensis. JOURNAL OF PHYCOLOGY 2015; 51:321-331. [PMID: 26986527 DOI: 10.1111/jpy.12276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/02/2014] [Indexed: 06/05/2023]
Abstract
Glycerol-3-phosphate (G3P) has been suggested as a novel regulator of plant defense signaling, however, its role in algal resistance remains largely unknown. The glycerol kinase (also designated as NHO1) and NAD-dependent G3P dehydrogenase (GPDH) are two key enzymes involved in the G3P biosynthesis. In our study, we cloned the full-length cDNA of NHO1 (NHO1Ph ) and GPDH (GPDHP h ) from the red alga Pyropia haitanensis (denoted as NHO1Ph and GPDHP h ) and examined their expression level under flagellin peptide 22 (flg22) stimulation or heat stress. We also measured the level of G3P and floridoside (a downstream product of G3P in P. haitanensis) under flg22 stimulation or heat stress. Both NHO1Ph and GPDHP h shared high sequence identity and structural conservation with their orthologs from different species, especially from red algae. Phylogenetic analysis showed that NHO1s and GPDHs from red algae were closely related to those from animals. Under flg22 stimulation or heat stress, the expression levels of NHO1Ph and GPDHP h were up-regulated, G3P levels increased, and the contents of floridoside decreased. But the floridoside level increased in the recovery period after heat stress. Taken together, we found that G3P metabolism was associated with the flg22-induced defense response and heat stress response in P. haitanensis, indicating the general conservation of defense response in angiosperms and algae. Furthermore, floridoside might also participate in the stress resistance of P. haitanensis.
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Affiliation(s)
- Xiao-Juan Lai
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Rui Yang
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Qi-Jun Luo
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Juan-Juan Chen
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Min Chen
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xiao-Jun Yan
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, 315211, China
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Miller JJ, Delwiche CF. Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome. Mar Genomics 2015; 21:31-42. [PMID: 25746767 DOI: 10.1016/j.margen.2015.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 02/11/2015] [Accepted: 02/22/2015] [Indexed: 10/23/2022]
Abstract
Emiliania huxleyi is a haptophyte alga of uncertain phylogenetic affinity containing a secondarily derived, chlorophyll c containing plastid. We sought to characterize its relationships with other taxa by quantifying the bipartitions in which it was included from a group of single protein phylogenetic trees in a way that allowed for variation in taxonomic content and accounted for paralogous sequences. The largest number of sequences supported a phylogenetic relationship of E. huxleyi with the stramenopiles, in particular Aureococcus anophagefferens. Far fewer nuclear sequences gave strong support to the placement of this coccolithophorid with the cryptophyte, Guillardia theta. The majority of the sequences that did support this relationship did not have plastid related functions. These results suggest that the haptophytes may be more closely allied with the heterokonts than with the cryptophytes. Another small set of genes associated E. huxleyi with the Viridiplantae with high support. While these genes could have been acquired with a plastid, the lack of plastid related functions among the proteins for which they code and the lack of other organisms with chlorophyll c containing plastids within these bipartitions suggests other explanations may be possible. This study also identified several genes that may have been transferred from the haptophyte lineage to the dinoflagellates Karenia brevis and Karlodinium veneficum as a result of their haptophyte derived plastid, including some with non-photosynthetic functions.
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Affiliation(s)
- John J Miller
- Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - Charles F Delwiche
- Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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Choi YH, Yamaguchi K, Oda T, Nam TJ. Chemical and mass spectrometry characterization of the red alga Pyropia yezoensis chemoprotective protein (PYP): protective activity of the N-terminal fragment of PYP1 against acetaminophen-induced cell death in Chang liver cells. Int J Mol Med 2014; 35:271-6. [PMID: 25374159 DOI: 10.3892/ijmm.2014.1992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/31/2014] [Indexed: 11/06/2022] Open
Abstract
In the present study, the chemical structure and chemoprotective activity of Pyropia yezoensis protein (PYP) were investigated using sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, automated protein sequencing, matrix-assisted laser desorption/ionization-quadrupole ion trap-time-of-flight mass spectrometry and a chemoprotective assay using a synthetic peptide. The PYP fraction was demonstrated to contain two proteins: PYP1 (10 kDa, SDS-resistant dimer) and PYP2 (10 kDa). PYP1 is a novel protein showing sequence homology with the hypothetical function-unknown proteins of Chondrus crispus (Rhodophyta) and Emiliania huxleyi (Haptophyceae). PYP2 is a paralog of an extrinsic protein of photosystem II found in other Rhodophyta. The synthetic peptide PYP1 (1-20), corresponding to the N-terminal 20 residues of PYP1 (ALEGGKSSGGGEATRDPEPT), exhibits chemoprotective activity against acetaminophen-induced cell death in Chang liver cells, indicating that PYP1 is a chemoprotectant of the PYP fraction. A possible association between the structure of PYP and its chemoprotective activity is discussed.
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Affiliation(s)
- Youn Hee Choi
- Institute of Fisheries Sciences, Pukyong National University, Busan 619‑911, Republic of Korea
| | - Kenichi Yamaguchi
- Graduate School of Science and Technology, Nagasaki University, Nagasaki 852‑8521, Japan
| | - Tatsuya Oda
- Graduate School of Science and Technology, Nagasaki University, Nagasaki 852‑8521, Japan
| | - Taek Jeong Nam
- Institute of Fisheries Sciences, Pukyong National University, Busan 619‑911, Republic of Korea
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Masuda T, Yamamoto A, Toyohara H. The iron content and ferritin contribution in fresh, dried, and toasted nori, Pyropia yezoensis. Biosci Biotechnol Biochem 2014; 79:74-81. [PMID: 25315337 DOI: 10.1080/09168451.2014.968087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Iron is one of the essential trace elements for humans. In this study, the iron contents in fresh, dried, and toasted nori (Pyropia yezoensis) were analyzed. The mean iron content of fresh, dried, and toasted nori were 19.0, 22.6, and 26.2 mg/100 g (dry weight), respectively. These values were superior to other food of plant origin. Furthermore, most of the iron in nori was maintained during processing, such as washing, drying, and toasting. Then, the form of iron in fresh, dried, and toasted nori was analyzed. As a result, an iron storage protein ferritin contributed to iron storage in raw and dried nori, although the precise rate of its contribution is yet to be determined, while ferritin protein cage was degraded in the toasted nori. It is the first report that verified the ferritin contribution to iron storage in such edible macroalgae with commercial importance.
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Affiliation(s)
- Taro Masuda
- a Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
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Kaňa R, Kotabová E, Lukeš M, Papáček S, Matonoha C, Liu LN, Prášil O, Mullineaux CW. Phycobilisome Mobility and Its Role in the Regulation of Light Harvesting in Red Algae. PLANT PHYSIOLOGY 2014; 165:1618-1631. [PMID: 24948833 PMCID: PMC4119043 DOI: 10.1104/pp.114.236075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/17/2014] [Indexed: 05/03/2023]
Abstract
Red algae represent an evolutionarily important group that gave rise to the whole red clade of photosynthetic organisms. They contain a unique combination of light-harvesting systems represented by a membrane-bound antenna and by phycobilisomes situated on thylakoid membrane surfaces. So far, very little has been revealed about the mobility of their phycobilisomes and the regulation of their light-harvesting system in general. Therefore, we carried out a detailed analysis of phycobilisome dynamics in several red alga strains and compared these results with the presence (or absence) of photoprotective mechanisms. Our data conclusively prove phycobilisome mobility in two model mesophilic red alga strains, Porphyridium cruentum and Rhodella violacea. In contrast, there was almost no phycobilisome mobility in the thermophilic red alga Cyanidium caldarium that was not caused by a decrease in lipid desaturation in this extremophile. Experimental data attributed this immobility to the strong phycobilisome-photosystem interaction that highly restricted phycobilisome movement. Variations in phycobilisome mobility reflect the different ways in which light-harvesting antennae can be regulated in mesophilic and thermophilic red algae. Fluorescence changes attributed in cyanobacteria to state transitions were observed only in mesophilic P. cruentum with mobile phycobilisomes, and they were absent in the extremophilic C. caldarium with immobile phycobilisomes. We suggest that state transitions have an important regulatory function in mesophilic red algae; however, in thermophilic red algae, this process is replaced by nonphotochemical quenching.
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Affiliation(s)
- Radek Kaňa
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Eva Kotabová
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Martin Lukeš
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Stěpán Papáček
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Ctirad Matonoha
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Lu-Ning Liu
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Ondřej Prášil
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
| | - Conrad W Mullineaux
- Institute of Microbiology, Centre Algatech, Academy of Sciences of the Czech Republic, 379 81 Trebon, Czech Republic (R.K., E.K., M.L., O.P.);Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, Branišovská 31, 370 05 Ceske Budejovice, Czech Republic (R.K., E.K., O.P.); Faculty of Fisheries and Protection of Waters, Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Complex Systems, University of South Bohemia in Ceske Budejovice, Zámek 136, 373 33 Nove Hrady, Czech Republic (Š.P.);Institute of Computer Science, Academy of Sciences of the Czech Republic, 18207 Praha 8, Czech Republic (C.M.); andSchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (L.-N.L., C.W.M.)
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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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Silva MY, Hughey JR. Complete mitochondrial genome of the holotype specimen of Wildemania schizophylla (Bangiales: Rhodophyta). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1001-2. [PMID: 24938105 DOI: 10.3109/19401736.2014.926524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ion Proton data was used to assemble the complete mitochondrial genome from the holotype specimen of Wildemania schizophylla (29,156 bp). The mitogenome contains 50 genes, including 2 ribosomal RNA, 23 transfer RNA, 4 ribosomal proteins, 2 ymfs, 3 open reading frames (ORFs), and 19 genes involved in cellular respiration. Although gene synteny is conserved, the mitogenome of W. schizophylla is significantly smaller due to the lack of large intronic ORFs present in the cytochrome oxidase locus of other Bangiales. The results support the recognition of Wildemania as distinct from Porphyra, and demonstrate that small amounts of type material are suitable for genomic studies.
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Affiliation(s)
- Mayra Y Silva
- a Division of Mathematics, Science, and Engineering , Hartnell College , Salinas , CA , USA
| | - Jeffery R Hughey
- a Division of Mathematics, Science, and Engineering , Hartnell College , Salinas , CA , USA
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Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes. Sci Rep 2014; 4:5113. [PMID: 24894641 PMCID: PMC4044621 DOI: 10.1038/srep05113] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/13/2014] [Indexed: 11/21/2022] Open
Abstract
Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm2 of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.
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Tajima N, Sato S, Maruyama F, Kurokawa K, Ohta H, Tabata S, Sekine K, Moriyama T, Sato N. Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum. JOURNAL OF PLANT RESEARCH 2014; 127:389-97. [PMID: 24595640 DOI: 10.1007/s10265-014-0627-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/05/2014] [Indexed: 05/11/2023]
Abstract
We determined the complete nucleotide sequence of the plastid genome of the unicellular marine red alga Porphyridium purpureum strain NIES 2140, belonging to the unsequenced class Porphyridiophyceae. The genome is a circular DNA composed of 217,694 bp with the GC content of 30.3%. Twenty-nine of the 224 protein-coding genes contain one or multiple intron(s). A group I intron was found in the rpl28 gene, whereas the other introns were group II introns. The P. purpureum plastid genome has one non-coding RNA (ncRNA) gene, 29 tRNA genes and two nonidentical ribosomal RNA operons. One rRNA operon has a tRNA(Ala)(UGC) gene between the rrs and the rrl genes, whereas another has a tRNA(Ile)(GAU) gene. Phylogenetic analyses suggest that the plastids of Heterokontophyta, Cryptophyta and Haptophyta originated from the subphylum Rhodophytina. The order of the genes in the ribosomal protein cluster of the P. purpureum plastid genome differs from that of other Rhodophyta and Chromalveolata. These results suggest that a large-scale rearrangement occurred in the plastid genome of P. purpureum after its separation from other Rhodophyta.
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Affiliation(s)
- Naoyuki Tajima
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan,
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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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