• Mycobiology
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• v.49 no.3
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• pp.267-274
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• 2021

Two Diaporthe species isolated from fruit of Citrus sinensis in China were characterized based on morphology and multilocus phylogeny of ITS, tef1, and tub2 gene sequences. The phylogeny indicated that the two species match Diaporthe taoicola and D. siamensis. A critical examination of phenotypic characteristics confirmed the phylogenetic results. Diaporthe taoicola was morphologically characterized by producing Alpha conidia with tapering toward both ends. Meanwhile, D. siamensis produced cylindrical or ellipsoidal Alpha conidia with two oil drops. Pathogenicity tests revealed that both species were pathogenic to fruit of C. sinensis. To our knowledge, the two species were firstly reported on Citrus sinensis in China.

• Journal of Species Research
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• v.10 no.2
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• pp.142-153
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• 2021

Algal genomics approaches provide a massive number of genome/transcriptome sequences and reveal the evolutionary history vis-à-vis primary and serial endosymbiosis events that contributed to the biodiversity of photosynthetic eukaryotes in the eukaryote tree of life. In particular, phylogenomic methods using several hundred or thousands of genes have provided new insights into algal taxonomy and systematics. Using this method, many novel insights into algal species diversity and systematics occurred, leading to taxonomic revisions. In addition, horizontal gene transfers (HGTs) of functional genes have been identified in algal genomes that played essential roles in environmental adaptation and genomic diversification. Finally, algal genomics data can be used to address the pangenome, including core genes shared among all isolates and partially shared strain-specific genes. However, some aspects of the pangenome concept (genome variability of intraspecies level) conflict with population genomics concepts, and the issue is closely related to defining species boundaries using genome variability. This review suggests a desirable future direction to merge algal pangenomics and population genomics beyond traditional molecular phylogeny and taxonomy.

• Mycobiology
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• v.49 no.1
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• pp.15-23
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• 2021

Two fungal strains (KNU-JJ-1827 and KNU-JJ-1829) belonging to the class Dothideomycetes were discovered from Jeju Island, Korea during this investigation of soil microfungi. Strain KNU-JJ-1827 showed fewer conidial septations, larger conidiogenous cells, and smaller conidia compared to the previously identified closest species of Didymocyrtis. Strain KNU-JJ-1829 revealed the similar characteristics of the nearest certain species of the genus Parathyridaria with the production of conidiogenous cells and conidia, because no asexual morphs were detected from the closest type strain Parathyridaria rosae. The novelty of the strains was also confirmed by analyzing molecular data using internal transcribed spacer regions and 28S rDNA. The molecular phylogeny also strongly support the detailed description and illustration for each proposed species as Didymocyrtis septata sp. nov. (KNU-JJ-1827) and Parathyridaria ellipsoidea sp. nov. (KNU-JJ-1829) isolated from soil in Korea.

• BMB Reports
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• v.41 no.3
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• pp.217-222
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• 2008

Based on a five-letter model of the 20 amino acids, we propose a new 2-D graphical representation of protein sequence. Then we transform the 2-D graphical representation into a numerical characterization that will facilitate quantitative comparisons of protein sequences. As an application, we construct the phylogenetic tree of 56 coronavirus spike proteins. The resulting tree agrees well with the established taxonomic groups.

• The Korean Journal of Mycology
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• v.49 no.1
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• pp.1-10
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• 2021

A survey of fungal diversity in Gyeongsang Province, Korea, revealed two previously unreported Aspergillus isolates, named KMG411 and KMG412. The phylogeny of the isolates was analyzed based on β-tubulin (BenA) and calmodulin (CaM) sequencing. Morphological analyses further identified the KMG411 and KMG412 as A. insuetus and A. nomius, respectively. Here we provide detailed morphological descriptions of the previously unrecorded Aspergillus species.

• The Korean Journal of Mycology
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• v.51 no.4
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• pp.307-311
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• 2023

Powdery mildew anamorphs were collected from Orixa japonica (Rutaceae) in Korea. Based on the morphology and molecular phylogeny derived from the internal transcribed spacer regions and the large subunit gene of the rDNA, the fungus was identified as Erysiphe orixae. This powdery mildew species has been known to be endemic to Japan. This is the first report on E. orixae in Korea.

• Animal Systematics, Evolution and Diversity
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• v.12 no.2
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• pp.121-136
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• 1996

In order to understand affinities and phylogeny of three families of the Superfamily Entomobryoidea allozyme analysis was performed with three species presumably representing each family, in addition to four species belonging to the neighboring Superfamily Poduroidea together. Electrophoresis for this purpose produced data for calculating allele frequency and enabled to obtain genetic distance and to depict dendrograms as well. The species of Isotomidae, Entomobryidae and Tomoceridae were clustered together whereas those of Hypogastruridae, Onychiuridae and Neanuridae were grouped as monophylies, respectively. Even though Tomoceridae and Entomobryidae were brought together they are considered complete families by showing high genetic distance value between them, thus supporting the hypothesis on their affinity among others. Gulgastrura reticulosa has been revealed to be separated from Hypogastruridae by being clustered rather with Onychiuridae. However, its high genetic distance value suggests the status as an independent family. The present result agreed with the phylogeny of Suborder Arthropleona divided into two Superfamilies mentioned above as in conventional systematics and also when compared with analysis of data of their morphological characters as well as 18S rDNA performed and published elsewhere by the present writers.

• Molecules and Cells
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• v.20 no.1
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• pp.151-156
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• 2005

The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.

• ALGAE
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• v.27 no.4
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• pp.225-234
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• 2012

Zygnema is a conjugating filamentous green algal genus that is distributed in a broad range of freshwater habitats, from sea level to alpine summits. Although more than 150 species have been described worldwide, their taxonomy remains unclear, probably owing to their relatively simple morphology. We investigated the detailed morphology of Korean Zygnema species, combined with analysis of the plastid psbA gene from 22 specimens of the genus and putative relatives, in order to develope a key to their identification and isolation, and to determine their relationships. We recognized two species of Zygnema; Z. insigne and Z. leiospermum, based on morphological characters such as width of the vegetative cell, position of zygospores, dimensions and form of spores, shape of female gametangia, and color of mesospores. The analysis of psbA data was consistent with morphological comparison. The pairwise divergence between two species was 3.7-4.1% (34-38 bp) in psbA sequences. The phylogeny of psbA revealed the monophyly of Z. insigne and Z. leiospermum together with two isolates of Z. circumcarinatum from Germany and Scotland. This is the first report on the psbA gene phylogeny of Zygnema.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1016-1023
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• 2008

Lichens are predominant and important components of flora in the terrestrial ecosystem of Antarctica. However, relatively few researches on the phylogenetic position of Antarctic lichen-forming fungi have been accomplished. In this study, partial sequences of nuclear large subunit rDNAs from 50 Antarctic specimens were obtained and the phylogeny was reconstructed. Antarctic lichen species were distributed in 4 orders, including the monophyletic order Agyrales, paraphyletic orders Pertusariales and Teloschistales, and polyphyletic order Lecanorales. Species diversity was highest in the order Lecanorales, followed by Teloschistales and Pertusariales. Based on the phylogeny and sequence similarity analyses, it is proposed that the taxonomy of Stereocaulon alpinum, Physcia caesia, Usnea aurantiacoatra, and Cladonia species should be revised by careful examination of their phenotypic and molecular characteristics. Six species known to be endemic to Antarctica, Catillaria corymbosa, Himantormia lugubris, Leptogium puberulum, Pertusaria pertusa, Rhizoplaca aspidophora, and Umbilicaria antarctica, formed unique lineages, implying independent origins in the Antarctic area.