• Mycobiology
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• 제36권4호
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• pp.203-210
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• 2008

In previous studies investigating the genus Xanthoparmelia, thirteen different species have been reported from South Korea alone. However, there currently has been no revisional study performed until now. To explore the genus Xanthoparmelia, a phenotypic analysis was performed based on morphological, anatomical and chemical characters, while an investigation of Xanthoparmelia phylogeny was based on nuclear ribosomal (nr) DNA ITS sequences. A thorough examination of the specimens deposited in the Korean Lichen Research Institute (KoLRI) confirmed that eight species of Xanthoparmelia occur inside South Korea. Our analysis further confirmed the colors of the lower surface and medullar chemistry are important taxonomic characters in Xanthoparmelia. This study also presents a detailed description of each species and a key to the genus.

• ALGAE
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• 제36권4호
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• pp.333-340
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• 2021

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.

• Animal cells and systems
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• 제2권4호
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• pp.451-454
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• 1998

Gulgastrura reticulosa, first described by Yosii (1966) as a monotypic new genus from a Korean limestone cave, was reviewed for its systematic position by c1adistic analysis of morphological characteristics, investigation of its intermaulting period and reproductive cycle as well as allozyme and 18S rDNA analysis. The great extent of divergence was strongly suggested by its combined lack of sensory organs (third antennal organ, postantennal organ, eyes, pseudocelli) with simultaneous development of an 'apical organ'at the tip of the antennae. The obvious divergence from any existing Collembola families was additionally supported by the extremely prolonged intermoulting period as well as by the low strap value it showed with Onychiuridae as obtained by 18S DNA sequence analysis. All these were considered Justifying the creation of a new family, Gulgastruridae, but still revealing more allied to Onychiuvidae rather than to Hypogastruridae.

• Journal of Microbiology
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• 제35권3호
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• pp.159-164
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• 1997

The phylogenetic study of Penicilium chrysogenum was performed based on amino acid sequence comparison of chitin synthase. Phylogenetic trees were constructed with the deduced amino acid sequences of the highly conserved region of chitin synthease gene fragments amplified by PCR. The BlasP similarity searcch and the bootstrap analysis of the deduced amino acid sequences of chitin synthase from P. chrysogenum with those form other fungi showed a close evolutionary relationship of Penicillium to ascomycetous fungi, especially to genus Aspergilus. The result from bootstrap analysis of the deduced amino acid sequences of the Class II chitin synthase from ascomyceteous fungi supported the usefulness of the Class II chitin synthease for phylogenetic study of filamentous fungi.

• The Plant Pathology Journal
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• 제35권4호
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• pp.389-392
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• 2019

The studies on detection of the Strawberry mottle virus (SMoV) have been conducted in Poland for breeding programme purpose and for producers of strawberry plant material. Leaf samples collected from infected strawberry plants were grafted on Fragaria sp. Indicators which were maintained in greenhouse for further study. Seven Fragaria vesca var. semperflorens 'Alpine' indicators infected by SMoV were used for the study aimed on molecular characterization of virus isolates. Partial RNA2 was amplified from total nucleic acids using the RT-PCR method. The obtained amplicons separately digested with BfaI, FauI, HaeIII, HincI, and TaqI enzymes showed different restriction profiles. The nucleotide sequences analysis of RNA2 fragment confirmed the genetic diversity of the SMoV isolates as their similarity ranged from 94.7 to 100%. Polish isolates shared 75.7-99.2% identity with sequence of the virus strains from the Czech Republic, the Netherlands, and Canada. Phylogenetic analysis resulted in grouping of the isolates found in Poland together with one of the Czech strain whereas two other from the Czech and the strains from the Netherlands and Canada created the separate cluster.

• ALGAE
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• 제19권3호
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• pp.153-160
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• 2004

The intergeneric relationship of Staurastrum complex including genus Arthrodesmus and Xanthidium was studied on the basis of mitochondrial coxⅢ sequence variation. Teiling's suggestion that Staurodesmus was an independent genus apart from genus Staurastrum, Arthrodesmus and Cosmarium was also reevaluated. The phylogeny inferred from coxⅢ gene was not consistent with morphological characteristics of Staurastrum complex. Genus Staurastrum was closely related to genus Xanthidium in the phylogenetic analysis of coxⅢ, but distant to genus Staurodesmus. The taxonomic treatment of genus Staurodesmus as an independent entity could not be determined, because Staurodesmus did not firm a monophyletic Glade. Therefore, genus Staurodesmus could not be treated as an independent genus as Prescott et al. (1982) claimed.

• Journal of Microbiology and Biotechnology
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• 제21권6호
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• pp.567-573
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• 2011

We investigated the phylogenetic diversity of ammoniaoxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by the cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster-1 could carry amoA sequences of environmental amoA cluster-3.

• ALGAE
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• 제21권3호
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• pp.283-286
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• 2006

This study carried out phylogenetic analysis of dinoflagellate Gonyaulax polygramma which was responsible for a harmful algal bloom episode in Korea in 2004. Molecular phylogenetic tree inferred from the partial LSU rDNA data showed that G. polygramma came up among the monophyletic Gonyaulax clade, but did not have apparent genetic affiliation to other Gonyaulax species. This result appears to be consistent with characteristic morphological features of G. polygramma such as epitheca sharply tapering to the apex and thecal plates ornamented with numerous longitudinal striations.

• Journal of Microbiology
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• 제34권3호
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• pp.215-219
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• 1996

Eight strains of Trichaptun (Polyporaceae), two strains from each species of T. abietinum, T. biforme, T. fusco-violaceum, and T. laricinum were examined to see their phylogenetic relationship by digesting mitochondrial DNAs with EcoRV, Hind III, XbaI, and PstI, and then analyzing fragmentation patterns with the methods of Nei and Li. T. abietinum, T. biforme, and T. laricinum developed an independent phylogenetic lineage, respectively, but T. fusco-violaceum FP-133997-sp showed a close relationship with two strains of T. bioforme, and T. fusco-violaceum HHB-4016-sp barely grouped with those of T. laricinum. Based on the results of the RFLP analysis of mtDNA, it is concluded that T. fusco-violaceum is under way to differentiation into two different subgroups.

• Fisheries and Aquatic Sciences
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• 제13권4호
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• pp.272-277
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• 2010

Seagrasses are marine angiosperms of ecological importance in providing shelter and food to aquatic species as well as maintaining the carbon cycle on earth. Phyllospadix iwatensis is a seagrass of the family Zosteraceae and is distributed along the eastern coast of Korea. The nucleotide sequences of P. iwatensis nuclear genes encoding 18S ribosomal RNA (rRNA) and internal transcribed spacer-1 (ITS-1) were determined for molecular phylogenetic analysis. Genomic DNA was isolated from P. iwatensis and used for PCR amplification of 18S rRNA and ITS-1. Examination of the 18S rRNA sequence of P. iwatensis showed a close (99% similarity) relationship to Zostera noltii, another genus of Zosteraceae, but a distant (84% similarity) evolutionary relationship to other macroalgal Laminariales species. Further discrepancies found in ITS-1 nucleotide sequences between closely related species indicate that the sequence information could be used for species identification.