• Journal of Veterinary Science
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• 제23권5호
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• pp.73.1-73.8
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• 2022

Background: Lumpy skin disease (LSD), a disease transmitted by direct and indirect contact with infected cattle, is caused by the Lumpy skin disease virus (LSDV). The disease affects cattle herds in Africa, Europe, and Asia. The clinical signs of LSD range from mild to the appearance of nodules and lesions in the skin leading to severe symptoms that are sometimes fatal with significant livestock economic losses. Objectives: This study aimed to characterize LSDV strains in the blood of infected cattle in Thailand based on the GPCR gene and determine the phylogenetic relationship of LSDV Thailand isolates with published sequences available in the database. Methods: In total, the blood samples of 120 cattle were collected from different farms in four provinces in the northeastern part of Thailand, and the occurrence of LSDV was examined by PCR based on the P32 antigen gene. The genetic diversity of LSDV based on the GPCR gene was analyzed. Results: Polymerase chain reaction assays based on the P32 antigen gene showed that 4.17% (5/120) were positive for LSDV. All positive blood samples were amplified successfully for the GPCR gene. Phylogenetic analysis showed that LSDV Thailand isolates clustered together with LSDVs from China and Russia. Conclusions: The LSD outbreak in Thailand was confirmed, and a phylogenetic tree was constructed to infer the branching pattern of the GPCR gene from the presence of LSDV in Thailand. This is the first report on the molecular characterization of LSDV in cattle in Thailand.

• ALGAE
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• 제38권1호
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• pp.1-22
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• 2023

An enormous body of research is focused on finding ways to commercialize carotenoids produced by the unicellular green alga, Haematococcus, often without the benefit of a sound phylogenetic assessment. Evidence of cryptic diversity in the genus means that comparing results of pigment studies may be confounded by the absence of a phylogenetic framework. Moreover, previous work has identified unnamed strains that are likely candidates for species status. We reconstructed the phylogeny of an expanded sampling of Haematococcus isolates utilizing data from nuclear ribosomal markers (18S rRNA gene, 26S rRNA gene, internal transcribed spacer [ITS]-1, 5.8S rRNA gene, and ITS-2) and the rbcL gene. In addition, we gathered morphological, ultrastructural and pigment data from key isolates of Haematococcus. Our expanded data and taxon sampling support the concept of a new species, H. privus, found exclusively in North America. Despite overlap in numerous morphological traits, results indicate that ratios of protoplast length to width and akinete diameter may be useful for discriminating Haematococcus lineages. High growth rate and robust astaxanthin yield indicate that H. rubicundus (SAG 34-1c) is worthy of additional scrutiny as a pigment source. With the description of H. privus, the evidence supports the existence of at least five, species-level lineages in the genus. Our phylogenetic assessment provides the tools to frame future pigment investigations of Haematococcus in an updated evolutionary context. In addition, our investigation highlighted open questions regarding polyploidy and sexuality in Haematococcus which demonstrate that much remains to be discovered about this green flagellate.

• 식물분류학회지
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• 제53권2호
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• pp.157-165
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• 2023

Paraphlomis koreana (Lamiaceae) was newly named and added to Korean flora in 2014. Paraphlomis belongs to the tribe Paraphlomideae, along with Ajugoides and Matsumurella. However, a recent study has suggested that P. koreana is morphologically similar to Matsumurella chinensis, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of P. koreana within the tribe and compare its genetic relationship with M. chinensis. We sequenced an additional complete plastid genome for an individual of P. koreana and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of P. koreana. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (rpl16 intron, rpl32-trnL, rps16 intron, and trnL-F) covering 13 Paraphlomis species and M. chinensis were conducted. Phylogenetic analyses concordantly supported that P. koreana forms a monophyletic group with M. chinensis. Moreover, our study revealed that P. koreana includes nrDNA sequences of M. chinensis as minor intra-individual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of P. koreana within Paraphlomis should be reconsidered.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.210-210
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• 2022

Silybum marianum is an annual or biennial plant from the Asteraceae family. It can grow in low-nutrient soil and drought conditions, making it easy to cultivate. From the seed, a specialized plant metabolite called silymarin (flavonolignan complex) is produced and is known to alleviate the liver from hepatitis and toxins damages. To infer the phylogenetic placement of a Korean milk thistle, we conducted a chloroplast assembly and annotation following by a comparison with existing Chinese reference genome (NC_028027). The chloroplast genome structure was highly similar with an assembly size of 152,642 bp, an 153,202 bp for Korean and Chinese milk thistle respectively. Moreover, there were similarities at the gene level, coding sequence (n = 82), transfer RNA (n = 31) and ribosomal RNA (n = 4). From all coding sequences gene set, the phylogenetic tree inference placed the Korean cultivar into the milk thistle clade; corroborating the expected tree. Moreover, an investigation the tree based only on the ycf1 gene confirmed the same tree; suggesting that ycf1 gene is a potential marker for DNA barcoding and population diversity study in milk thistle genus. Overall, the provided data represents a valuable resource for population genomics and species-centered determination since several species have been reported in the Silybum genus.

• Journal of Ginseng Research
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• 제44권4호
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• pp.637-643
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• 2020

Background: Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.

• 생명과학회지
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• 제18권6호
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• pp.753-758
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• 2008

원추리속(Genus Hemerocallis) 식물은 초본이며 일부 종은 약용으로 매우 중요하다. 이 속내 8개 분류군에 대해 ISSR (inter simple sequence repeats) 마커로 계통학적 관계를 분석하였다. 조사한 식물은 원추리(Hemerocallis fulva), 왕원추리(H. fulva for. kwanso), 각시원추리(H. dumortieri), 골잎원추리(H. coreana), 홍도원추리(H. hongdoensis), 큰원추리(H. middendorffi), 노랑원추리(H. thunbergii), 애기원추리(H. minor)이다. 또한 이들 분류군에 대한 유전적 변이와 구조를 조사하였다. 종간 유전적 다양도는 $0.068{\sim}0.123$이며 평균 유전적 다양도는 0.098로 전반적으로 낮았다. 애기원추리가 가장 높은 값을 나타내었다. 세대 당 이주하는 개체수는 매우 적었다(Nm=0.128). 원추리속 종은 계통도에서 세 분지군으로 나누어졌다. 한 그룹은 H. fulva, H. fulva for. kwanso, H. middendorffi였다. 다른 그룹은 Hemerocallis, H. dumortieri, H. thunbergii, H. minor였다. 나머지는 H. coreana와 H. hongdoensis로 두 번째 그룹과 자매군을 형성하였다. 비록 종 내 적은 개체수로 분석하였지만 원추리속 식물종이 ISSR 마커로 잘 분리되었다.

• Animal Systematics, Evolution and Diversity
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• 제18권1호
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• pp.165-179
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• 2002

백만종을 넘어 천만종에 이를 것으로 추산되는 절지동물 (Phylum Arthropoda)은 지구상에 현존하는 가장 번성한 동물군 중의 하나로서 캠브리아기 생물의 빅뱅 이후 급변하는 환경속에서도 멸종의 길을 걷지 않고 성공적으로 살아남아 오늘날의 다양성을 유지하고 있다. 멸종한 절지동물인 삼엽충(Trilobita)을 제외하면, 현재 서식하고 있는 절지동물들은 다섯 아문으로 나누어진다: 육각류(Hexapoda), 갑각류(Crustacea), 다지류(Myriapoda) 협각류 (Chelicerata), 바다거미류(Pycnogonida), 계통분류학자들은 절지동물과 인접분류군들 (arthropod relatives) -유조동물(Onychophora), 완보동물(Tardigrada), 오구동물(Pentastomida)-의 상호 유연관계와 선구통물 내에서의 계통학적 위치들, 절지동물의 단계통성 혹은 다계통성, 절지동물의 주요 다섯 아문들 간의 계통유연관계 등에 관한 논쟁들을 지난 세기 내내 이어왔다. 최근에 선구등불을 크게 탈피동물 (Ecdysozoa)과 촉수담륜동물 (Lophotrochozoa)로 나누고 탈피동물 내에서 절지동물의 인접분류군 중의 하나가 선형동물 (Nematoda)일 수 있다는 새로운 동물 계통이 발표된 바 있다. 본 종설에서는 이 체계를 기본으로하여 선구동물 내에서의 절지동물과 그 인접분류군들의 계통학적 위치 및 상호유연관계를 우선적으로 언급하므로서 문(Phylum) 준위에서의 절지동물 계통에 관한 논쟁들을 소개하고자 한다. 그 연후에 적지동물의 단계통성에 관한 논쟁, 절지동물 주요 네 그룹 (아문)간의 계통유연관계에 관한 논쟁들에 초점을 맞추어 논하고자 한다. 절지동물의 주요 다섯 아문 중 하나인 바다거미류 (상대적으로 작은 분류군임)의 경우, 다른 주요 네 그룹 (Euarthropoda)의 자매 군으로서 가장 원시적인 형태의 절지류인지, 아니면 협각류의 자매군인지가 논란이 되고는 있을지라도 본 종설에서는 비중있게 다루지 않았다.

• Parasites, Hosts and Diseases
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• 제52권2호
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• pp.205-209
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• 2014

Echinococcus granulosus is the causative agent of cystic echinococcosis with medical and veterinary importance in China. Our main objective was to discuss the genotypes and genetic diversity of E. granulosus present in domestic animals and humans in western China. A total of 45 hydatid cyst samples were collected from sheep, humans, and a yak and subjected to an analysis of the sequences of mitochondrial cytochrome b (cytb) gene. The amplified PCR product for all samples was a 1,068 bp band. The phylogenetic analysis showed that all 45 samples were identified as E. granulosus (genotype G1). Ten haplotypes were detected among the samples, with the main haplotype being H1. The haplotype diversity was 0.626, while the nucleotide diversity was 0.001. These results suggested that genetic diversity was low among our samples collected from the west of China based on cytb gene analysis. These findings may provide more information on molecular characteristics of E. granulosus from this Chinese region.

• 한국균학회지
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• 제43권1호
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• pp.13-19
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• 2015

낙동강 지류의 하천에 자생하는 5종류의 수생식물인 마름, 물억새, 미나리, 부들, 및 줄을 채집하였다. 수생식물의 뿌리에서 분리된 34균주의 내생균류는 ITS영역 염기 서열을 분석하였다. 분리된 모든 내생균류들에 대하여 다양성 지수와 계통분석을 수행하였다. 내생균류는 17속으로서, Acremonium속, Alternaria속, Aspergillus속, Cladosporium속, Emericellopsis속, Fusarium속, Galactomyces속, Leptosphaeria속, Microsphaeropsis속, Penicillium속, Peyronellaea속, Phoma속, Pseudeurotium속, Rhizomucor속, Talaromyces속, Trematosphaeria속, Zalerion속 등이 분리되었다. 5종류의 수생식물에서 Alternaria, Talaromyces속의 균류들이 비교적 많이 분포하고 있었다. 본 연구는 낙동강 지류의 하천 습지에 자생하는 수생식물 군락에서 공생하는 내생균류의 다양성에 대한 연구이다.

• 한국작물학회지
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• 제59권4호
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• pp.492-497
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• 2014

Soybean (Glycine max L.) is crucial legume crop as source of high quality vegetable protein and oil, and Korea is regarded as a part of center of soybean origin. To expand the information of conserved genetic diversity, we analyzed the genetic variability of soybean collection mainly introduced Korean accessions using 75 microsatellite markers. A total of 1,503 alleles with an average value of 20.0 alleles were detected among 644 accessions. Korean collection revealed average allele number of 13.4 while Chinese, Japanese and Southeast Asian accessions showed 9.0, 5.4 and 6.5 mean alleles, respectively. Especially, Korean accessions showed more number of private allele per locus as 3.4 contrary to other geographical groups. The mean expected heterozygosity and polymorphic information content was 0.654 and 0.616, respectively, and expected heterozygosity values were not significantly distinguished according to the geographical groups. The phylogenetic dendrogram and deduced population structure based on DNA profiles of 75 SSR loci showed Korean accessions formed distinct gene pool against Chinese accessions, and could be divided into five subpopulations. Korean soybean accessions have specific genetic diversity and might be serve the valuable alleles for bio-industry as a part of the center of soybean origin.