• BMB Reports
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• 제32권4호
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• pp.414-418
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• 1999

A novel gene for malonyl-CoA decarboxylase was discovered in the mat operon, which encodes a set of genes involved in the malonate metabolism of Rhizobium trifolii (An and Kim, 1998). The subunit mass determined by SDS-PAGE was 53 kDa, which correspond to the deduced mass from the sequence data. The molecular mass of the native enzyme determined by field flow fractionation was 208 kDa, indicating that R. trifolii malonyl-CoA decarboxylase is homotetrameric. R. trifolii malonyl-CoA decarboxylase converted malonyl-CoA to acetyl-CoA with a specific activity of 100 unit/mg protein. Methylmalonyl-CoA was decarboxylated with a specific activity of 0.1 unit/mg protein. p-Chloromercuribenzoate inhibited this enzyme activity, suggesting that thiol group(s) is(are) essential for this enzyme catalysis. Database analysis showed that malonyl-CoA decarboxylase from R. trifolii shared 32.7% and 28.1% identity in amino acid sequence with those from goose and human, respectively, and it would be located in the cytoplasm. However, there is no sequence homology between this enzyme and that from Saccharopolyspora erythreus, suggesting that malonyl-CoA decarboxylases from human, goose, and R. trifolii are in the same class, whereas that from S. erythreus is in a different class or even a different enzyme, methylmalonyl-CoA decarboxylase. According to the homology analysis, Cys-214 among three cysteine residues in the enzyme was found in the homologous region, suggesting that the cysteine was located at or near the active site and plays a critical role in catalysis.

• 대한바이러스학회지
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• 제28권4호
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• pp.303-316
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• 1998

An attenuated classical swine fever virus (CSFV), Suri strain, is a variant derived from a vaccine virus, LOM strain. This study was performed to elucidate the molecular biologcal properties of CSFV Suri strain, and to obtain the basic data for molecular epidemiological approaches for the disease. The truncated form of gp55 gene without the C-terminal transmembrane domain, in size of 1,023bp, was amplified by RT-PCR and sequenced by dye terminator cyclic sequencing method, and inserted into BamHI site of pAcGP67B baculovirus vector, establishing a cloned pAcHEG plasmid. By the nucleotide sequences determined, 341 amino acid sequences were predicted. As compared the nucleotide and amino acid sequences of gp55 of Suri with the various CSFV, Suri strain showed the high homology over 99.1% with ALD and LOM strains, but comparably the lower homology with Alfort and Brescia. In comparison of amino acid sequence in variable domain of gp55 protein, the similar tendency of homology was observed. In hydrophobicity analysis, all of four CSFV strains revealed the analogous patterns of hydrophobicity. The numbers and locations of N-glycosylation site and cysteine residues in gp55 were analyzed, those of Suri strain being coincident with ALD and LOM strains. The results suggest that gp55 in Suri strain has the high similarity to those in ALD and LOM strains in terms of the nucleotide and amino acid sequences and the functional properties of gp55 protein.

• Mycobiology
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• 제47권4호
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• pp.527-532
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• 2019

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (M_AF) and the average number of alleles (N_A) were 0.50 and 5.47, respectively. The average number of genotypes (N_G), observed heterozygosity (H_O), expected heterozygosity (H_E), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson's correlation coefficient showed that M_AF was negatively correlated with N_G (-0.683), N_A (-0.600), H_O (-0.584), and PIC (-0.941). N_G, N_A, H_O, and PIC were positively correlated with other polymorphic parameters except for M_AF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

• 식물분류학회지
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• 제40권4호
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• pp.234-239
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• 2010

핵 리보좀 DNA ITS 구간의 염기서열 정보를 이용하여 한국산 산형과 개발나물속의 분자 계통학적 연구를 수행하였다. ITS 계통수는 한반도 고유종인 대암개발나물(S. heterophyllum)이 한반도에 생육이 보고된바 없는 러시아 우수리지역의 고유종인 S. tenue와 동일한 종임을 밝혔다. ITS 1과 ITS 2 구간의 염기서열 비교시 S. tenue와 인천 문수산에 생육하고 있는 대암개발나물이 100% 일치함을 확인할 수 있었다. 또한 ITS 구간의 염기서열은 최근 신종으로 발표된 세잎개발나물(S. ternifolium)이 개발나물속의 다른 분류군과 뚜렷하게 구별됨을 지지하고 있었다. 세잎개발나물은 유연관계가 가장 가까운 일본 고유종 S. serra의 ITS 염기서열 비교시 1.4와 1.6%의 차이점을 가지고 있음이 확인되어 종으로서의 처리가 적합함을 확인할 수 있었다.

• The Plant Pathology Journal
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• 제16권4호
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• pp.231-235
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• 2000

The 3,000 nucleotides of 3'-terminal region of the genomic RNA of a new isolate of carlavirus from a Korean native lily (Lilum lancitoium) was cloned and its nucleotide sequences were determined. The coat protein (CP) gene of the virus showed 72.0% to 72.8% nucleotide sequence identities and 86.9% to 88.0% amino acid sequence identities with those of the four strains (two Korean, one Dutch, and one Japanese isolates) of lily symptomless virus (LSV). Interestingly, different amino acid sequences between the new isolate and LSV strains were located at the N-terminal region of the CP. Pairwise amino acid sequence comparison of the CP gene revealed sequence identities of 22.0% to 71.1% between the virus and other 9 carlavirus species. The 25 kDa and 12 kDa proteins genes of the virus share 30.7% to 76.3% and 31.1% to 85.8% amino acid sequence identities, respectively, with those of 8 other carlaviruses. The 16 kDa protein gene of the virus shares 16.7% to 72.9% amino acid sequence identities with that of 9 other carlaviruses. These data indicate that the virus, designated as lily latent virus (LiLV), is a distinct of the Carlavirus genus and distinguished from the known strains of LSV.

• Molecules and Cells
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• 제20권3호
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• pp.416-422
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• 2005

We previously used Southern blot analysis to detect restriction-length polymorphisms between male fertile and cytoplasmic male sterile (CMS) cytoplasms at the coxII and atp6 loci of the mtDNA of Capsicum annuum L. Two copies of atp6 were found in each male fertile and CMS pepper lines. Interestingly, one of the copies of atp6 in CMS pepper was a 3'-truncated pseudogene. The open reading frame of the coxII gene was the same in the fertile (N-) and CMS (S-) lines. However, the nucleotide sequence in the S-cytoplasm diverged from that in the N-cytoplasm 41 bp downstream of the stop codon. To develop CMS-specific sequence-characterized amplified region (SCAR) markers, inverse PCR was performed to characterize the nucleotide sequences of the 5' and 3' flanking regions of mitochondrial atp6 and coxII from the cytoplasms of male fertile (N-) and CMS (S-) pepper plants. Based on these data, two CMS-specific SCAR markers, 607 and 708 bp long, were developed to distinguish N-cytoplasm from S-cytoplasm by PCR. The CMS-specific PCR bands were verified for 20 cultivars containing either N- or S-cytoplasm. PCR amplification of CMS-specific mitochondrial nucleotide sequences will allow quick and reliable identification of the cytoplasmic types of individual plants at the seedling stage, and assessment of the purity of $F_1$ seed lots. The strategy used in this report for identifying CMS-specific markers could be adopted for many other crops where CMS is used for F1 seed production.

• 한국약용작물학회지
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• 제25권6호
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• pp.411-417
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• 2017

Background: Adenophora triphylla var. japonica (Regel) H. Hara shows vegetative growth with radical leaves during the first year and shows reproductive growth with cauline leaves and bolting during the second year. In addition, the shape of the plant varies within the same species. For this reason, there are limitations to classifying the species by visual examination. However, there is not sufficient genetic information or molecular tools to analyze the genetic diversity of the plant. Methods and Results: Approximately 34.59 Gbp of raw data containing 342,487,502 reads was obtained from next generation sequencing (NGS) and these reads were assembled into 357,211 scaffolds. A total of 84,106 simple sequence repeat (SSR) regions were identified and 14,133 primer sets were designed. From the designed primer sets, 95 were randomly selected and were applied to the genomic DNA which was extracted from five plants and pooled. Thirty-nine primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis. Conclusions: The 39 novel SSR markers developed in this study could be used for the genetic diversity analysis, variety identification, new variety development and molecular breeding of A. triphylla.

• Parasites, Hosts and Diseases
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• 제56권2호
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• pp.175-181
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• 2018

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris-endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum, A. lumbricoides, and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides, A. suum, and the hybrid, but pigs were mainly infected with A. suum. This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.

• Fisheries and Aquatic Sciences
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• 제6권3호
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• pp.110-115
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• 2003

Expressed sequence tag (EST) analysis was conducted using a cDNA library made from the liver mRNA of olive flounder (Paralichthys olivaceus). In the survey of 421 ESTs, 362 showed significant homology to previously described genes while 59 were unidentified or novel. Comparative analysis of the identified ESTs showed that 69 $(19.0\%)$ clones were identified as homologous to the previously reported olive flounder ESTs, and 279 $(77.1\%)$ clones were identified as orthologs of known genes from other organisms. The remaining 14 $(3.9\%)$ clones were identified as orthologs of known sequences with unknown functions. These tagged cDNA clones, identified and unidentified, could provide fundamental baseline data for genomic studies of this species.

• 대한수의학회지
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• 제32권4호
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• pp.555-567
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• 1992

In this study gene encoding structural proteins of a CPV isolate was cloned and sequenced to elucidate the molecular genetical properties of the canine parvoviruses isolated from the field. Six recombinant plasmids of pEP3, p1471, p2070, pEP069, pEP338 and p14711p were constructed from the map positions 22 to 98 of RF DNA to clone the VP1 and VP2 genes of CPV-V20. Sequentialy the gene comprising 3780 nucleotides were sequenced by dideoxy chain termination method. When nucleotide sequence of gene encoding the structural proteins of CPV-V20 was compared with those of other strains, CPV-N, CPV-d and CPV-780929 published previously, DNA, homologies to CPV-V20 were 99.87% with CPV-N, 99.73% with CPV-d, 96.85% with CPV-780929 and 98.4% with FPLV-Carl, respectively. The DNA sequence data of CPV-V20 showed seven point mutations and also deletion of 135 nucleotides from the nucleotide position 4745 to 4879 located in the 3'-noncoding region of CPV-N.