• Title/Summary/Keyword: nuclear SSU rDNA

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Nuclear DNA Quantification of Some Ceramialean Algal Spermatia by Fluorescence Microscopic Image Processing and their Nuclear SSU rDNA Sequences

  • Choi, Han-Gu;Lee, Eun-Young;Oh, Yoon-Sik;Kim, Hyung-Seop;Lee, In-Kyu
    • ALGAE
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    • v.19 no.2
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    • pp.79-90
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    • 2004
  • Nuclear DNA contents of spermatia from eight ceramiacean and four dasyacean algae (Ceramiales, Rhodophyta) and microspores from two land plants were estimated by fluorescence microscopic image processing and their nuclear SSU rDNA sequence data were analyzed. In frequency distribution patterns, the DAPI-stained nuclear volume (NV) of spermatia showed two peaks corresponding to 1C and 2C. Nuclear 2C DNA contents estimated from NV were 0.45-2.31 pg in ceramiacean and 0.40-0.57 pg in dasyacean algae and 8.42-9.51 pg in two land plants, Capsicum annuum and Nicotiana tabacum. By nuclear patterning of vegetative cells derived from an apical cell, 2C DNA contents of spermatia were 2.31 pg in an alga having uninucleate and non-polyploid nucleus (Aglaothamnion callophyllidicola), 0.45-1.94 pg in algae having uninucleate and polyploid nucleus (Antithamnion spp. and Pterothamnion yezoense), and 0.40-0.62 pg in algae having multinucleate and non-polyploid nuclei (Griffithsia japonica and dasyacean algae). Each mature spermatium and microspore (pollen grain) seemed to have a 2C nucleus, which may provide a genetic buffering system to protect the genetic content of a spermatium and microspore from potentially lethal mutations. Nuclear DNA content and SSU rDNA sequence of Antithamnion sparsum from Korea were reasonably different from those of Antithamnion densum from France. The data did not support the previous taxonomic studies that these two taxa could be conspecific.

Phylogenetic Relationships of the Aphyllophorales Inferred from Sequence analysis of Nuclear Small Subunit Ribosomal DNA

  • Kim, Seon-Young;Jung, Hack-Sung
    • Journal of Microbiology
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    • v.38 no.3
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    • pp.122-131
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    • 2000
  • Phylogenetic classification of the Aphyllophorales was conducted based on the analysis of nuclear small subunit ribosomal RNA (nuc SSU rDNA) sequence. Based on phylogenetic groupings and taxonomic characters, 16 families were recognized and discussed. Although many of the characters had more or less homoplasies, miroscopic characters such ad the mitic system and clamp, spore amyloidity and rot type appeared to be important in the classification of the Aphyllophorales. Phylogenetically significant families were newly defined to improve the classification of the order Aphyllophorales.

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Two Freshwater Cryptomonads New to Korea: Cryptomonas marssonii and C. pyrenoidifera

  • Kim, Jee-Hwan;Boo , Sung-Min;Shin, Woong-Ghi
    • ALGAE
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    • v.22 no.3
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    • pp.147-152
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    • 2007
  • We described two brownish freshwater Cryptomonas species, C. marssonii Skuja and C. pyrenoidifera Geitler as first records in Korea. The identification was based on light microscopy, scanning electron microscopy, and nuclear SSU rDNA sequences analysis. Cryptomonas marssonii is characterized by its sigmoid shape with a sharply pointed and dorsally curved antapex, dorso-ventrally flattened cell, two lateral plastids without pyrenoid, and its dimension of 18-25 μm in length and 8-13 μm in width. Cryptomonas pyrenoidifera is characterized by ovoid to elliptical shape with a partially twisted or rounded antapex, dorso-ventrally biconvex cell, lateral plastids with two pyrenoids, and the dimensions of 15-22 μm in length and 10-14 μm in width. Nuclear SSU rDNA sequences between C. marssonii WCK01 from Korea and CCAC0086 from Gernmay, and between C. pyrenoidifera WCK02 from Korea and CCMP152 from Australia were identical, respectively.

Morphology and phylogenetic relationships of two Antarctic strains within the genera Carolibrandtia and Chlorella (Chlorellaceae, Trebouxiophyceae)

  • Hyunsik Chae;Eun Jae Kim;Han Soon Kim;Han-Gu Choi;Sanghee Kim;Ji Hee Kim
    • ALGAE
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    • v.38 no.4
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    • pp.241-252
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    • 2023
  • The genera Carolibrandtia and Chlorella have been described as small green algae with spherical cell shapes that inhabit various environments. Species of these genera are often difficult to identify because of their simple morphology and high phenotypic plasticity. We investigated two small coccoid strains from Antarctica based on morphology, molecular phylogeny by two alignment methods which have been applied to previous phylogenetic studies of the genus Chlorella, and comparison of the secondary structures of nuclear small subunit (SSU) and internal transcribed spacer (ITS) rDNA sequences. Light microscopy of two strains revealed spherical cells containing chloroplasts with pyrenoids, and the morphological characteristics of the strains were nearly identical to those of other Chlorella species. However, based on the phylogenetic analyses of nuclear SSU and ITS rDNA sequences, it was determined that the Antarctic microalgal strains belonged to two genera, as the Chlorella and Carolibrandtia. In addition, the secondary structures of the SSU and ITS2 sequences were analyzed to detect compensatory base changes (CBCs) that were used to identify and describe the two strains. A unique CBC in the SSU rDNA gene was decisive for distinguishing strain CCAP 211/45. The ITS2 rDNA sequences for each strain were compared to those obtained previously from other closely related species. Following the comparison of morphological and molecular characteristics, we propose KSF0092 as a new species, Chlorella terrestris sp. nov., and the reassignment of the strain Chlorella antarctica CCAP 211/45 into Carolibrandtia antarctica comb. nov.

Phylogenetic analysis of pleurotus species based on the nuclear SSU rRNA sequences

  • Jeong, Jae-Hoon;Kim, Eun-Kyoung;Roe, Jung-Hye
    • Journal of Microbiology
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    • v.34 no.1
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    • pp.38-39
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    • 1996
  • The internal regions of nuclear small subunit rRNA from 6 plaeurotus species and 5 Pleurotus ostreatus strains were amplified by PCR and sequenced. The DNA sequences of 8 Pleurotus strains (P. ostreatus NFFA2, NFFA4501, NFFA4001, KFFA4001, KFCC11635, P florida, P. florida, P. sajor-cuju, P. pulmonarius, and P. spodoleucus) were idential, but P. cornucopiae differed from them in two bases out of 605 bases. However, p[hylogenetic analysis of the sequences by DNA-distance matrix and UPGMA methods showed that P. ostreatus NFFA2m1 and NFFA2m2, known as mutants of P. ostreatus NFFA2, belonged to anther group of Basidiomycotina, which is close to the genus Auricularia. The difference of the SSU rDNA sequences of P. cornucopiae from other Pleurotus species tested corresponds to the difference of mitochondrial plasmid type present in Pleurotus species as observed by Kim et al. (1993, Korean J. Microbiol. 31, 141-147).

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Phylogenetic Analysis of Pleurotus Species Based on the Nuclear SSU rRNA Sequences (Phylogenetic Analysis of Pleurotus Species Based on the Nuclear SSU rRNA Sequences)

  • Jeong, Jae Hun;Kim, Eun Gyeong;No, Jeong Hye
    • Journal of Microbiology
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    • v.34 no.1
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    • pp.37-37
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    • 1996
  • The internal regions of nuclear small subunit rRNA from 6 plaeurotus species and 5 Pleurotus ostreatus strains were amplified by PCR and sequenced. The DNA sequences of 8 Pleurotus strains (P. ostreatus NFFA2, NFFA4501, NFFA4001, KFFA4001, KFCC11635, P florida, P. florida, P. sajor-cuju, P. pulmonarius, and P. spodoleucus) were idential, but P. cornucopiae differed from them in two bases out of 605 bases. However, p[hylogenetic analysis of the sequences by DNA-distance matrix and UPGMA methods showed that P. ostreatus NFFA2m1 and NFFA2m2, known as mutants of P. ostreatus NFFA2, belonged to anther group of Basidiomycotina, which is close to the genus Auricularia. The difference of the SSU rDNA sequences of P. cornucopiae from other Pleurotus species tested corresponds to the difference of mitochondrial plasmid type present in Pleurotus species as observed by Kim et al. (1993, Korean J. Microbiol. 31, 141-147).ishement of silencing at the HMR/hsp82 locus can occur in G1-arrested cells. Cell cycle arrest at G1 phase was achieved by treatment of early log a cell cultures with .alpha.-factor mating pheromone, which induces G1 arrest. The result suggests that passage through S phase (and therefore DNA replication) is nor required for re-establishing silencer-mediated repression at the HMNRa/HSP82 locus. Finally, to test whether de nono protein synthesis is required for re-establishment of silencer-mediated repression, cells were pretreated with cycloheximide (500 /.mu.g/ml) 120 min. It was apparent that inhibiting protein synthesis delays, but does not prevent, re-establishment of silencer-mediated repression. Altogether, these results indicate that re-establishment of silencer-mediated repression is not dependent on the DNA replication and has no requirement for protein synthesis.

Phylogenetic relationships among Acanthamoeba spp. based on PCR-RFLP analyses of mitochondrial small subunit rRNA gene

  • Yu, Hak-Sun;Hwang, Mee-Yul;Kim, Tae-Olk;Yun, Ho-Cheol;Kim, Tae-Ho;Kong, Hyun-Hee;Chung, Dong-Il
    • Parasites, Hosts and Diseases
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    • v.37 no.3
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    • pp.181-188
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    • 1999
  • We investigated the value of mitochondrial small subunit rRNA gene (mt SSU rDNA) PCR-RFLP as a taxonomic tool for Acanthamoeba isolates with close inter-relationships. Twenty-five isolates representing 20 species were included in the analysis. As in nuclear 18s rDNA analysis, two type strains (A. astronyxis and A. tubiashi) of morphological group 1 diverged earliest from the other strains, but the divergence between them was less than in 18s riboprinting. Acanthamoeba griffini of morhological group 2 branched between pathogenic (A. culbertsoni A-1 and A. healyi OC-3A) and nonpathogenic (A.palestinensis Reich, A. pustulosa GE-3a, A. royreba Oak Ridge, and A lenticulata PD2S) strains of morphological group 3. Among the remaining isolates of morphological group 2, the Chang strain had the identical mitochondrial riboprints as the type strain of A. hatchetti. AA2 and AA1, the type strains of A. divionensis and A. paradivionensis, respectively, had the identical riboprints as A. quina Vil3 and A. castellanii Ma. Although the branching orders of A. castellanii Neff, A. polyphaga P23, A. triangularis SH621, and A. lugdunensis L3a were different from those in 18S riboprinting analysis, the results obtained from this study generally coincided well with those from 18S riboprinting. Mitochondrial riboprinting may have an advantage over nuclear 18S rDNA riboprinting beacuse the mt SSU rDNAs do not seem to have introns that are found in the 18S genes of Acanthamoeba and that distort phylogenetic analyses.

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Molecular Phylogenetic Relationships Within the Genus Alexandrium(Dinophyceae) Based on the Nuclear-Encoded SSU and LSU rDNA D1-D2 Sequences

  • Kim, Choong-Jae;Sako Yoshihiko;Uchida Aritsune;Kim, Chang-Hoon
    • Journal of the korean society of oceanography
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    • v.39 no.3
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    • pp.172-185
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    • 2004
  • LSU rDNA D1-D2 and SSU rDNA genes of 23 strains in seven Alexandrium (Halim) species, A. tamarense (Lebour) Balech, A. catenella (Whedon et Kofoid), A. fraterculus (Balech) Balech, A. affine (Inoue et Fukuyo) Balech, A. insuetum Balech, A. pseudogonyaulax (Biecheler) Horiguchi ex Yuki et Fukuyo and A. tamiyavanichii Balech, were sequenced and the data were used for molecular phylogenetic analysis. The sequence data revealed 11 and 7 ribotypes in the LSU rDNA D1-D2 region and 4 and 17 ribotypes in the SSU rDNA region of A. catenella and A. tamarense, respectively. Other Alexandrium species had also 1 to 5 ribotypes in the two regions. With the exception of CMC2 and CMC3 of A. catenella, all A. tamarense and A. catenella strains had a common ribotype, a functionally expressed rRNA gene (here termed type A), in both gene regions. In addition to the functionally expressed gene, several pseudogenes were obtained that were found to be good tools to analyze the population designation of regional isolates by grouping them according to shared ribotypes. From the phylogenetic analysis of the sequence data determined in this study and retrieved from GenBank, the genus Alexandrium was divided into 14 groups: 1) A. tamarense, 2) A. excavatum, 3) A. catenella, 4) Tasmanian A. tamarense, 5) A. affine (and/or A. concavum), 6) Thai A. tamarense, 7) A. tamiyavanichii, 8) A. fraterculus, 9) A. margalefii, 10) A. andersonii, 11) A. ostenfeldii, 12) A. minutum (or A. lusitanicum), 13) A. insuetum, and 14) A. pseudogonyaulax. The SSU rDNA gene sequence of A. fundyense was so similar to those of A. tamarense used in this study that the two species were difficult to discriminate each other. A. tamiyavanichii was closest to the A. tamarense strain isolated in Thailand and close to the long chain-forming species of A. affine and A. fraterculus. The phylogenetic tree showed that A. margalefii, A. andersonii, A. ostenfeldii, A. minutum and A. insuetum constituted the basal relative complex, and that A. pseudogonyaulax is an ancestral taxon in the genus Alexandrium.

Emendation of Rhodomonas marina (Cryptophyceae): insights from morphology, molecular phylogeny and water-soluble pigment in an Arctic isolate

  • Niels Daugbjerg;Cecilie B. Devantier
    • ALGAE
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    • v.39 no.2
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    • pp.75-96
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    • 2024
  • Rhodomonas (Cryptophyceae) and species assigned to this genus have undergone numerous taxonomic revisions. This also applies to R. marina studied here as it was originally assigned as a species of Cryptomonas and later considered a variation of R. baltica, the type species. Despite being described more than 130 years ago, R. marina still lacks a comprehensive characterization. Light and electron microscopy were employed to delineate a strain from western Greenland. The living cells were 18 ㎛ long and 9 ㎛ wide, elliptical in shape with a pointed to rounded posterior and truncated anterior in lateral view. Two sub-equal flagella emerged from a vestibulum, where also a furrow extended. In transmission electron microscopy, the furrow was associated with a tubular gullet and the pyrenoid embedded in a deeply lobed chloroplast. The chloroplast contained DNA in perforations and was surrounded by starch grains. A tubular nucleomorph was enclosed within the pyrenoid matrix. In scanning electron microscopy, the inner periplast consisted of rectangular plates with rounded edges and posteriorly these were replaced by a sheet-like structure. The water-soluble pigment was Crypto-Phycoerythrin type I (Cr-PE 545). A phylogenetic inference based on SSU rDNA confirmed the identity of strain S18 as a species of Rhodomonas as it clustered with congeners but also Rhinomonas, Storeatula, and Pyrenomonas. These genera formed a monophyletic clade separated from a diverse assemblage of other cryptophyte genera. To further explore the phylogeny of R. marina a concatenated phylogenetic analysis based on the SSU rDNA-ITS1-5.8S rDNA-ITS2-LSU rDNA region was performed but included only closely related species. The secondary structure of nuclear internal transcribed spacer 2 was predicted and compared to similar structures in related species. Using morphological and molecular signatures as diagnostic features the description of R. marina was emended.

Ansanella granifera gen. et sp. nov. (Dinophyceae), a new dinoflagellate from the coastal waters of Korea

  • Jeong, Hae Jin;Jang, Se Hyeon;Moestrup, Ojvind;Kang, Nam Seon;Lee, Sung Yeon;Potvin, Eric;Noh, Jae Hoon
    • ALGAE
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    • v.29 no.2
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    • pp.75-99
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    • 2014
  • A small dinoflagellate, Ansanella granifera gen. et sp. nov., was isolated from estuarine and marine waters, and examined by light microscopy, scanning electron microscopy, and transmission electron microscopy. In addition, the identity of the sequences (3,663-bp product) of the small subunit (SSU), internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), and D1-D3 large subunit (LSU) rDNA were determined. This newly isolated, thin-walled dinoflagellate has a type E eyespot and a single elongated apical vesicle, and it is closely related to species belonging to the family Suessiaceae. A. granifera has 10-14 horizontal rows of amphiesmal vesicles, comparable to Biecheleria spp. and Biecheleriopsis adriatica, but greater in number than in other species of the family Suessiaceae. Unlike Biecheleria spp. and B. adriatica, A. granifera has grana-like thylakoids. Further, A. granifera lacks a nuclear fibrous connective, which is present in B. adriatica. B. adriatica and A. granifera also show a morphological difference in the shape of the margin of the cingulum. In A. granifera, the cingular margin formed a zigzag line, and in B. adriatica a straight line, especially on the dorsal side of the cell. The episome is conical with a round apex, whereas the hyposome is trapezoidal. Cells growing photosynthetically are $10.0-15.0{\mu}m$ long and $8.5-12.4{\mu}m$ wide. The cingulum is descending, the two ends displaced about its own width. Cells of A. granifera contain 5-8 peripheral chloroplasts, stalked pyrenoids, and a pusule system, but lack nuclear envelope chambers, a nuclear fibrous connective, lamellar body, rhizocysts, and a peduncle. The main accessory pigment is peridinin. The SSU, ITS regions, and D1-D3 LSU rDNA sequences differ by 1.2-7.4%, >8.8%, and >2.5%, respectively, from those of the other known genera in the order Suessiales. Moreover, the SSU rDNA sequence differed by 1-2% from that of the three most closely related species, Polarella glacialis, Pelagodinium bei, and Protodinium simplex. In addition, the ITS1-5.8S-ITS2 rDNA sequence differed by 16-19% from that of the three most closely related species, Gymnodinium corii, Pr. simplex, and Pel. bei, and the LSU rDNA sequence differed by 3-4% from that of the three most closely related species, Protodinium sp. CCMP419, B. adriatica, and Gymnodinium sp. CCMP425. A. granifera had a 51-base pair fragment in domain D2 of the large subunit of ribosomal DNA, which is absent in the genus Biecheleria. In the phylogenetic tree based on the SSU and LSU sequences, A. granifera is located in the large clade of the family Suessiaceae, but it forms an independent clade.