• Molecules and Cells
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• v.27 no.3
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Journal of Plant Biotechnology
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• v.37 no.3
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• pp.275-282
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• 2010

Chloroplast transformation in higher plants offers many attractive advantages over nuclear transformation, including a high-level accumulation of foreign proteins, multi-gene expression in single transformation event via transgene stacking in operons and no position effect due to site-specific integration of transgenes by homologous recombination. Most importantly, chloroplast transgenic plants are eco-friendly because their transgenes are maternally inheritance in most crop plants. However, chloroplast transformation system has limited success in crops alike nuclear transformation. In the past two decades, great progress has been made to overcome the limitations of chloroplast transformation, thus expending chloroplast bioreactor to several important crops including soybean, carrot, lettuce, and oilseed. Therefore, it has become possible that chloroplast transformation of crops can be used not only for the improvement of agronomic traits, but also for the production of vaccines and high valuable therapeutic proteins in pharmaceutical industry.

• Journal of Species Research
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• v.6 no.1
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• pp.76-90
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• 2017

Aster altaicus var. uchiyamae Kitam. is an endemic taxon of Korea and is protected by law as an endanger taxon. The genetic information of A. altaicus var. uchiyamae is unavailable in Genbank. Here we sequenced chloroplast genome of A. altaicus var. uchiyamae. The cp-genome of Aster altaicus var. uchiyamae was 152,446 bps in size: LSC was 84,240 bps, IR 25,005 bps, SSC 18,196 bps. The cp-genome contains 112 genes and 21 introns consisted of 79 protein coding genes(PCGs), 4 RNA genes, and 29 tRNA genes, with 20 group II introns and one group I intron. There were three pseudo-genes including ${\psi}$-ycf1, ${\psi}$-rps19, and ${\psi}$-trnT_GGU. Eighteen genes, five introns, and parts of two genes and an intron are found within the IR, which has two copies. The cp-DNA of Aster altaicus var. uchiyamae is distinguished from A. spathulifolius, only known cp-genome of the genus Aster, by 172 SNP in genic regions of 43 PCGs and 21 indels in 11 PCGs and SSU. The chloroplast genome sequence was deposited at GenBank (KX35265).

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Journal of Plant Biotechnology
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• v.38 no.1
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• pp.42-48
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• 2011

Chloroplast genetic engineering of higher plants offers several unique advantages compared with nuclear genome transformation, such as high levels of transgene expression, a lack of position effect due to site-specific transgene integration by homologous recombination, multigene engineering in a single transformation event and reducing risks of gene flow via pollen due to maternal inheritance. We established a reproducible chloroplast transformation system of potato using a tobacco specific plastid transformation vector, pCtVG (trnI-Prrn-aadA-mgfp-TpsbA-trnA). Stable transgene integration into chloroplast genomes and the homoplasmic state of the transgenome were confirmed by PCR and Southern blot analyses. Northern, immunoblot analysis, and GFP fluorescence imaging revealed high expression and accumulation of GFP in the plastids of potato leaves. This system would provide new opportunities for genetic improvement and mass production of value added foreign proteins in this crop.

• ALGAE
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• v.18 no.2
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• pp.121-127
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• 2003

The pyrenoid ultrastructure and distribution of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and Rubisco activase in the chloroplasts of Chlamydomonas reinhardtii was studied using the immunogold localization technology with electron microscopy. There were several tubular thylakoids invading in the pyrenoid matrix to form several spokewise channels. The connections between pyrenoid matrix and stroma of chloroplast were the partial of channels. The starch sheath surrounding the pyrenoid was separated into several parts by the connections in transection. Some thylakoids were packed together near the connections in one side of the pyrenoid. Those special structures might be used to transport substance between pyrenoid and stroma of chloroplasts. With the antibody raised against the large subunits of Rubsico from C. protothecoides, the result of the gold immunolocalization of Rubisco in Chlamydomonas reinhardtii showed most of the gold particles heavily labeled the pyrenoid matrix, as well as the starch sheath matrix, and very few in the stroma of chloroplasts. The gold particle density was 880.00 $\pm$ 164.32, 190.00 $\pm$ 152.39 and 9.60 $\pm$ 5.37 ${\mu}m^{-2}$ in pyrenoid matrix, starch sheath and stroma region of chloroplast respectively (background: 5.67 $\pm$ 1.53 ${\mu}m^{-2}$). 99.59% of the total Rubiscos was calculated to be concentrated in the pyrenoid matrix and starch sheath by spatial densities. The gold immunolocalization of Rubisco activase also showed that Rubisco activase was mainly concentrated in the periphery of the pyrenoid and the starch sheath (the density was as high as 229.69 $\pm$ 96.96 ${\mu}m^{-2}$). There were very few gold particles located in the stroma of chloroplasts. These results indicated that pyrenoid surface and starch sheath was the site for Rubisco activation and $CO_2$ fixation, which supported the suggestion that pyrenoids perform photosynthesis function.

• ALGAE
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• v.34 no.2
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• pp.71-90
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• 2019

A new encrusting red alga was found growing abundantly on glass debris items that drifted ashore along the coasts of Oregon and Washington. These included discarded fluorescent tubes, incandescent light bulbs, capped liquor bottles, and ball-shaped fishing-net floats. Field collections and unialgal cultures of the alga revealed that it consisted of two morphological phases: a young loosely aggregated turf and a mature consolidated mucilaginous crust. The turf phase consisted of a basal layer of globose cells that produced erect, rarely branched, uniseriate to multiseriate filaments up to $500{\mu}m$ long with closely spaced cells lacking pit-plugs. These filaments expanded in size from their bases to their tips and released single cells as spores. At maturity, a second phase of growth occurred that produced a consolidated crust, up to $370{\mu}m$ thick. It consisted of a basal layer of small, tightly appressed ellipsoidal-to-elongate cells that generated a mucilaginous perithallial matrix containing a second type of filament with irregularly spaced cells often undergoing binary division. At the matrix surface, the original filaments continued to grow and release spores but often also eroded. Individual cells, examined using confocal microscopy and SYBR Green staining, were found to contain a central nucleus, a single highly lobed peripheral chloroplast without a pyrenoid, and numerous chloroplast nucleoids. Morphological data from field and culture isolates and molecular data (rbcL, psbA, and SSU) show that this alga is a new genus and species which we name Viator vitreocola, "a traveller on glass."

• ALGAE
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• v.23 no.2
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• pp.119-133
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• 2008

We cultured a tubular marine green alga, originally identified as Capsosiphon groenlandicus (J. Agardh) K.L. Vinogradova, from Amaknak Island, Alaska. The alga had an alternation of heteromorphic generations in which tubular monoecious fronds produced quadriflagellate zoospores and/or biflagellate isogametes. The gametes fused to produce cysts or Codiolum-like zygotes with long, tortuous stalks. Cysts and codiola produced 8-16 aplanospores, which germinated in situ to yield upright fronds. Fronds arising from both aplanospores and zoospores displayed a distinctive development in which non-septate colorless rhizoids from the base of the initially uniseriate, Ulothrix-like filament were transformed into septate uniseriate Ulothrix-like photosynthetic filaments. These transformed filaments then developed new basal non-septate rhizoids. This pattern of rhizoids becoming filaments, which then produced new rhizoids, was repeated to yield a tuft of up to 50 fronds. Periclinal and longitudinal divisions occurred in each filament, starting basally, until the mature tubular thallus was achieved. Pyrenoid ultrastructure revealed several short inward extensions of chloroplast lamellae, each of which was surrounded by pyrenoglobuli. Analysis of ribosomal SSU and ITS sequences placed this alga in the family Ulotrichaceae, order Ulotrichales, together with but as a distinct species from North Atlantic Capsosiphon groenlandicus. Analysis of a partial ITS sequence from authentic Capsosiphon fulvescens, the current name of the type of the genus Capsosiphon, indicated that neither our material nor C. groenlandicus belongs in that genus, and we propose a new genus, Pseudothrix, to accommodate both species. We propose P. borealis for the North Pacific entity formerly called C. groenlandicus and make the new combination P. groenlandica for the Atlantic species.

• ALGAE
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• v.39 no.2
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• pp.97-108
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• 2024

The Ralfsiaceae family, part of the Ralfsiales order and consisting of crustose brown algae, includes five genera: Analipus, Endoplura, Fissipedicella, Heteroralfsia, and Ralfsia. In this study, a novel crustose genus named Ramipedicella gen. nov. is introduced within the Ralfsiaceae based on molecular and morphological analyses. Phylogenetic analyses using both concatenated dataset (rbcL + COI-5P genes) and rbcL indicate that the crustose brown algae that we collected from Korea and Russia form a unique grouping within the Ralfsiaceae. This grouping is strongly supported by both bootstrap analysis and Bayesian posterior probabilities. The genetic differences in the rbcL and COI-5P sequences between Ramipedicella and other genera within Ralfsiaceae range from 6.7 to 9.3% for rbcL and from 15.5 to 20.8% for COI-5P. Ramipedicella is characterized by crustose thalli having new crusts growing on top of old ones with a hypothallial basal layer and erect perithallial filaments, long cells with width-to-length ratio of 1 : 1-16, single chloroplast per cell, plurangia with one to several sterile cells, one to several unangia produced from unicellular stalks or from the lateral-basal region to the paraphyses, and unangia arising sequencially in irregularly branched specialized filaments. Ramipedicella, the recently identified genus, comprises two distinct species. Ramipedicella miniloba, the type species, is distinguished by crusts with small lobes, numerous hair tufts, plurangia terminated by 1-4 sterile cells, and large oblong unangia. Ramipedicella longicellularis is identified by generally smooth crusts, absence of phaeophycean hairs, plurangia terminated by 1-2 apical sterile cells, and smaller mostly oblanceolate unangia.

• ALGAE
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• v.21 no.4
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• pp.407-416
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• 2006

Low molecular weight carbohydrates, phycobilin pigments and cell structure using light and transmission electron microscopy were used to describe a new genus of unicellular red algae, Erythrolobus coxiae (Porphyridiales, Porphyrideophyceae, Rhodophyta). The nucleus of Erythrolobus is located at the cell periphery and the pyrenoid, enclosed by a cytoplasmic starch sheath, is in the cell center. The pyrenoid matrix contains branched tubular thylakoids and four or more chloroplast lobes extend from the pyrenoid along the cell periphery. A peripheral encircling thylakoid is absent. The Golgi apparatus faces outward at the cell periphery and is always associated with a mitochondrion. Porphyridium and Flintiella, the other members of the Porphyrideophyceae, also lack a peripheral encircling thylakoid and have an ER-mitochondria-Golgi association. The low molecular weight carbohydrates digeneaside and floridoside are present, unlike both Porphyridium and Flintiella, which have only floridoside. The phycobilin pigments B-phycoerythrin, R-phycocyanin and allophycocyanin are present, similar to Porphyridium purpureum. The cells have a slow gliding motility without changing shape and do not require substrate contact. The ultrastructural features are unique to members of the Porphyrideophyceae and recent molecular analyses clearly establish the validity of this new red algal class and the genus Erythrolobus.