• ALGAE
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• 제37권3호
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• pp.205-211
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• 2022

The trend in naming genera based almost exclusively on molecular data, and not on morphological diagnostic characters, is increasing. In bifurcating phylogenetic trees generic cut-offs are arbitrary, but at the bare minimum nomenclatural changes should be supported by multiple phylogenetic methodologies using appropriate models for all the various gene partitions, strong support with all branch support methods, and should also result in adding to our knowledge of the interrelationships of taxa. We believe that a recent taxonomic treatment of the genus Pyropia (Yang et al. 2020) into several genera is unwarranted. We reanalysed the data presented in the recent article, using additional phylogenetic methods. Our results show that many of the newly established genera are not well supported by all methods, and the new circumscription of the genus Pyropia renders it unsupported. We also tested additional outgroups, which were previously suggested as sister to Pyropia, but this did not substantially change our conclusions. These generic nomenclatural changes of the previously strongly supported genus Pyropia, do not shed light on the evolution of this group and have serious consequences in these commercially important algae, that are also governed by a plethora of regulation and by-laws that now need to be amended. We suggest that the over-splitting of groups based only on poorly produced and modestly supported phylogenies should not be accepted and that the genus Pyropia sensu Sutherland et al. (2011) be restored.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제3권4호
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• pp.221-226
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• 2022

A filarial nematode was found in a blood sample of an Anas falcata individual collected in South Korea in 2018. Phylogenetic analysis based on partial cytochrome C oxidase subunit I (COI) sequences placed the nematode as a novel genus of the family Onchocercidae and as closely related to Mansonella species, Chandlerella quiscali, and filarial nematodes recently reported in avian species. However, different phylogenetic relationship was observed in the NADH dehydrogenase subunit 5 and 12S rRNA-based phylogenetic trees, which might indicate the filarial nematode found in this study was not defined to belong to the known specific genera of the family Onchocercidae. The screening of 105 additional avian blood samples retrieved only one 12S rRNA-targeting polymerase chain reaction (PCR)-positive sample, which indicates that filarial nematode infection is rare in wild birds or that it occurs below the detection limit of PCR in blood samples. Nevertheless, considering the recent findings about ancient interactions between birds and human pathogenic filarial nematodes and their pathogenic potential in several avian species, additional exploration of novel filarial nematodes in wild birds remains necessary.

• 한국어류학회지
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• 제18권4호
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• pp.293-299
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• 2006

두툽상어 (Scyliorhinus torazame)부터 분리된 항산화 효소 Cu,Zn-superoxide dismutase (Cu,Zn-SOD 또는 SOD1)의 핵산 염기서열 및 추정 아미노산 서열을 대상으로 분자 계통학적 분석을 실시하였다. 종래 알려져 있는 척추동물의 Cu,Zn-SOD 서열들을 포함하여 neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) 및 Bayesian 분석 등을 포함한 다양한 계통 분석을 수행하였으며, 이를 통해 연골어류인 본 어종의 척추동물 분류군 내에서의 계통적 위치를 추정하고자 하였다. 다양한 분자 계통수로부터 얻어진 대부분의 consensus tree들에서 분석에 사용한 분류군들은 종래 알려진 분류학적 위치와 비교적 잘 일치하였고, 이중 두툽상어는 같은 연골어류종인 blue shark와 높은 유연관계를 나타내면서 보다 진화한 경골어류들과는 확연히 구분되는 분지를 형성하였다. 특히 핵산 염기서열을 바탕으로 한 neighbor-joining 분석에서 두툽상어는 경골어류와 양막동물에 비해 보다 원시형태의 척추동물 Cu,Zn-SOD 유전자의 한 형태를 보유하고 있는 것으로 나타났다.

• Molecules and Cells
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• 제25권4호
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• pp.510-522
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• 2008

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

• 한국약용작물학회지
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• 제17권1호
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• pp.46-53
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• 2009

Schizonepeta spike (Korean name "Hyung-Gae") has been used for oriental medicinal purposes in Korea, China and Japan. In this study, twenty six "Hyung-Gae" samples were collected including nine certified Schizonepeta tenuifolia plants, and seventeen commercially marketed "Hyung-Gae" products. Chloroplast trnL-F and rDNA ITS regions of the "Hyung-Gae" samples were sequenced and used to identify whether the samples were genuine S. tenuifolia or not. As the result, the trnL-F and ITS sequences of all the "Hyung-Gae" samples were shown to be identical and it was proven that commercially available medicinal products "Hyung-Gae" are genuine S. tenuifolia. Phylogenetic tree of S. tenuifolia using the trnL-F sequences was constructed and compared with phylogenetic tree using ITS of rDNA region sequences. In these tree, S. tenuifolia was affiliated in the family Lamiaceae. It is proven that trnL-F and ITS phylogenetic trees are useful to study taxonomic position of S. tenuifolia.

• 식물분류학회지
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• 제46권2호
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• pp.247-255
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• 2016

천주교 대구교구청에 심어져 있는 오래된 왕벚나무의 기원을 추적하기 위하여 제주도에 자생하는 야생 왕벚나무와 재배 왕벚나무(Somei-yoshino cherry)의 계통분류학적 유연관계를 알아보았다. 한국과 일본에서 채집한 야생 왕벚나무, 재배 왕벚나무 및 근연종인 올벚나무, 총 25 개체에 대하여 cpDNA 두 구간(rpl16 유전자, trnS-trnG intergenic spacer)의 염기서열을 사용하여 계통수와 반수체형(haplotype) 네트워크를 작성하여 두 분류군을 비교하였다. 야생 왕벚나무와 재배 왕벚나무는 서로 구별되는 분류군으로 드러났으며, 비록 적은 샘플을 대상으로 비교적 짧은 유전자위가 사용되었지만 야생 왕벚나무는 재배 왕벚나무보다 반수체형 다양성이 높은 것으로 나타났다. 이는 야생 왕벚나무의 교배 기원에 모계쪽으로 기여한 것으로 알려진 올벚나무의 유전적 다양성에서 기인하는 것으로 추정된다. 따라서, 야생 왕벚나무와 재배 왕벚나무의 계통분류학적 관계를 보다 명확하게 파악하기 위하여 올벚나무를 한국과 일본의 다양한 분포 지역에서 넓게 채집하여 추가 연구를 실시할 필요가 있다고 생각된다. Taquet 신부가 제주에서 채집하여 대구에 옮겨 심었다고 추정되었던 천주교 대구교구청의 오래된 왕벚나무는 야생 왕벚나무가 아닌 재배 왕벚나무로 보는 것이 타당하다.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.143.1-143
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• 2003

Hop stunt viroid(HSVd) is a plant pathogen which infect a number of hosts such as grapevine, Citrus and Prunus plants. Sequence variants of HSVd have been divided into three types(i. grapevine and hop, ii. citrus, iii. plum, peach, apricot and almond). Purified RNAs from plum trees were used for the synthesis of cDNA with reverse transcription and amplified by polymerase chain reaction. Cloned cDNAs were sequenced and two different consensus sequence variants were detected. A neighbor-joining analysis was carried out on the sequence variants together with 62 previously described variants of HSVd from hop, plum and other species. Sequence variants from plum trees cultivated in Korea were clustered in HSVd-plum subtype and not in HSVd-hop subtype which were two Korean isolates belongs. These relationship between sequence variants from plum and two Korean isolates in HSVd-hop type supports the other origin for hop stunt disease.

• 식물분류학회지
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• 제44권1호
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• pp.39-50
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• 2014

엽록체 matK 유전자와 핵 ITS 염기서열을 이용하여 나도풍란속 및 풍란속의 계통학적 위치를 정립하였다. 또한, 이들 마커를 이용하여 종 및 원산지 추적에 활용가능성을 평가하였다. 풍란속과 나도풍란속은 두 마커 모두에서 뚜렷한 단계통군을 형성하였다. 풍란속의 자매군은 Vanda임이 두 마커 모두에서 입증되었으나,본 연구 결과는 풍란속을 Vanda에 포함시키는 처리에는 동의하지 않았다. 나도풍란속은 (Dimorphorchis (Pteroceras (Saccolabiun+Phalaeonopsis))) 계통군과 자매군을 형성하였고, 이중 Dimorphorchis와 자매속일 가능성이 가장 높았다. 형태적 유사성으로 나도풍란속이 Aerides와 자매속이라는 주장의 가능성은 희박하였다. 두 마커를 분석한 결과 풍란속의 경우 종 및 종 내의 산지별 구별이 가능한 것으로 평가되었다. 따라서 풍란의 재배 개체들의 기원을 규명하는데도 유용한 것으로 평가되었다. 그러나, 공공 염기서열 DB에 있는 서열들은 의유전자로 추정되는 서열들을 다수 포함하고 있었다. 또한, 재배 난과식물에는 속간 및 종간 잡종이 많으며 잡종에 의한 수평적 유전자 이동문제 등이 결부되어 있으므로, 계통학적으로 염기서열 자료를 이용하는데 주의하여야 한다. 계통분석을 위하여는 한 종 내의 여러 개체로부터 염기서열을 확보하는 것이 이러한 위험성을 줄이는 방법 중에 하나이다.

• Animal cells and systems
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• 제11권2호
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• pp.147-153
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• 2007

DNA extracted from ancient bones of Cervidae animals was examined to identify the species and to determine the phylogenetic relationships to those from extant cervids. Abundant ancient bones were excavated from Kumsung archaeological site in Jeju Island, Korea, and were identified as Cervidae animals based on morphological features of their antlers and lower mandibles. Their mitochondrial DNA (mtDNA) control region (CR) was partially sequenced and subsequently compared with those previously reported in database. The results confirmed that the ancient sequences are lineage of Cervidae. On the phylogenetic trees constructed using the sequence diversity of the CR sequences of family Cervidae, the ancient DNA sequences were found on distinct clusters. The ancient sequences were located in the subfamily Capreolinae cluster, and six ancient sequences were closely related to those of extant Korean roe deer in Jeju Island and Korean Peninsula. Consequently, the results of this study suggest that the roe deer inhabited Jeju Island in ancient times. However, there is no evidence for the existence of subfamily Cervinae, including Sika deer, while it has been described in several historical records. The results suggest that this finding could contribute to understanding of the origin and phylogenetic relationships of extant and ancient roe deer on Jeju Island.

• Tuberculosis and Respiratory Diseases
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• 제81권3호
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• pp.216-221
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• 2018

Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.