• 식물병연구
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• 제28권2호
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• pp.98-107
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• 2022

The incidence of Tomato brown rugose fruit virus (ToBRFV) and biological and molecular characterization of the Palestinian isolates of ToBRFV are described in this study. Symptomatic leaf samples obtained from Solanum lycopersicum L. (tomatoes) and Nicotiana tabacum L. (cultivated tobacco) plants were tested for tobamoviruses infection by reverse transcription polymerase chain reaction. Tomato leaf samples collected from Tulkarm and Qalqilia are infected with ToBRFV-PAL with an infection rate of 76% and 72.5%, respectively. Leaf samples collected from Jenin and Nablus were found to be mixed infected with ToBRFV-PAL and Tobacco mosaic virus (TMV) (100%). Sequence analysis of the ToBRFV-PAL genome showed that the net average nucleotide divergence between ToBRFV/F48-PAL strain and the Israeli and Turkish strains was 0.0026398±0.0006638 (±standard error of mean), while it was 0.0033066±0.0007433 between ToBRFV/F42-PAL and these two isolates. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with the TMV. The sequenced Palestinian isolates of ToBRFV-PAL shared the highest nucleotide identity with the Israeli ToBRFV isolate suggesting that the virus was introduced to Palestine from Israel. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV which would help in the management of the disease.

• The Plant Pathology Journal
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• 제22권3호
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• pp.265-270
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• 2006

Cultivated hot pepper crops showing severe mosaic symptom were found in Korea in 2004 and their causal agent was identified as Cucumber mosaic virus (CMV). These pepper crops was resistant to the virus in the filled, and they belonged to pathotype 0 (P0) resistant pepper. Resistance screening of selected pepper plants showed that a pepper isolate of CMV was the P0 resistance-breaking virus. This P0 resistance-breaking isolate of CMV, named as Ca-P1, was isolated from leaves of the virus-infected Capsicum annuum cv. Manidda that showed systemic severe mosaic symptom. Ca-P1-CMV could induce systemic mosaic symptoms on P0-susceptible (P0-S) and P0-resistant (P0-R) cultivars whereas an ordinary strain (Fny-CMV) could not infect P0-R. This result suggests that Ca-P1-CMV can overcome P0 resistant pepper cultivars. To analyze its genome sequence, the complete nucleotide sequence of RNA3 of Ca-P1-CMV was determined from the infectious full-length cDNA clone of the virus. RNA3 of Ca-P1-CMV consisted of 2,219 nucleotides. Overall sequence homology of RNA3-encoded two viral proteins (movement protein and coat protein) revealed high similarity (75.2-97.2%) with the known CMV strains. By sequence analysis with known representative strains of CMV, Ca-P1-CMV belongs to a typical member of CMV subgroup IB. The resistance and resistance-breaking mechanisms of pepper and counterpart CMV, respectively, remain to be investigated, which will enrich the genetic resources and accelerate CMV-resistant pepper breeding programs.

• Molecules and Cells
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• 제23권2호
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• pp.145-153
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• 2007

Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.

• 환경생물
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• 제41권1호
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• pp.1-13
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• 2023

잠두위조바이러스2 (BBWV2)는 경제적으로 중요한 원예, 관상작물에 심각한 피해를 주는 바이러스 중의 하나다. BBWV2의 넓은 기주 범위, 매개충 방제의 어려움 등 효과적인 치료제가 없기 때문에, 병을 예방하거나 저항성 품종의 개발 등을 위해서는 BBWV2의 새로운 분리주들의 특성 조사와 연구가 필요하다. 본 연구에서는 2019년 금산지역의 잎들깨 재배농가에서 분리된 BBWV2 분리주(BBWV2-GS-PF)의 유전학적·생물학적 특성을 구명하고 기존에 보고된 분리주들과의 특성을 비교하였다. 순수 분리된 BBWV2-GS-PF는 기존 분리주와 달리 들깨에서 심한 모자이크 증상과 고추에서 원형 반점 증상을 보였다. BBWV2-GS-PF의 유전자 계통분석 결과, 기존에 알려진 2개의 그룹과 약 76~80%의 비교적 낮은 유전자 상동성을 보이며 계통이 분화된 것을 확인할 수 있었다.

• 한국미생물·생명공학회지
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• 제49권1호
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• pp.111-119
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• 2021

본 연구에서는 국내 자생 식물인 아욱으로부터 새로운 균주를 분리 및 동정하였고 해당 미생물이 생산하는 항미생물질의 활성과 관련 생합성 유전자들을 확인하고자 하였다. 16S rRNA 유전자 서열 정보를 토대로 비교한 결과, 아욱에서 분리된 균주는 Bacillus velezensis이었으며 strain은 MV2라고 명명되었다. 유전체 염기서열 분석을 통해 전체 유전정보를 확인할 수 있었으며, 45.57% GC 함량을 가지는 4,191,702 bp 크기의 1개 컨티그(contig)가 존재하는 것으로 확인되었다. B. velezensis MV2가 정지기에 생산하는 물질 중 항균 활성이 확인된 소수성 물질 분획을 이용하여 항균 활성 스펙트럼 테스트를 진행한 결과, 그람음성균보다 그람양성균에서 더 높은 억제능이 확인되었다. 6종의 곰팡이를 이용한 항진균 활성 테스트에서는 모든 진균에 대해 강한 저해 활성을 보였으며, 특히 F. fujikuroi와 F. graminearum에 대한 항진균 활성이 매우 강하게 나타났다. 세균에 대한 항균물질의 작용 기작 분석을 통해 해당 항균물질은 균을 용해시키는 살균(bactericidal) 특성을 가진 것으로 추측할 수 있었다. B. velezensis MV2의 유전체 염기서열 정보를 통해 이차대사산물 생합성 유전자 cluster를 탐색한 결과 총 47가지 이차대사산물 생산이 예측되었으며, 기존에 밝혀져 있는 물질들과 유사도 80% 이상인 물질은 14개로 확인되었다. 앞서 확인된 내용들을 바탕으로 B. velezensis MV2에서 생성되는 항균물질은 비리보솜 펩타이드성 물질로 예상되며, 향후 항균물질의 동정과 활용 가능성에 대한 추가적인 연구가 필요할 것으로 생각되었다. 기존에 상업적으로 이용되었던 곰팡이에 대한 활성이 낮은 항균물질 생물제제들과 함께 복합기능성 미생물제로 활용하여 식품산업 및 농업에서의 이용 가능성이 있음을 보여주었다.

• Journal of Microbiology and Biotechnology
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• 제28권11호
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• pp.1916-1927
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• 2018

Corynebacterium glutamicum is an excellent platform for the production of amino acids, and is widely used in the fermentation industry. Most industrial strains are traditionally obtained by repeated processes of random mutation and selection, but the genotype of these strains is often unclear owing to the absence of genomic information. As such, it is difficult to improve the growth and amino acid production of these strains via metabolic engineering. In this study, we generated a complete genome map of an industrial L-valine-producing strain, C. glutamicum XV. In order to establish the relationship between genotypes and physiological characteristics, a comparative genomic analysis was performed to explore the core genome, structural variations, and gene mutations referring to an industrial L-leucine-producing strain, C. glutamicum CP, and the widely used C. glutamicum ATCC 13032. The results indicate that a 36,349 bp repeat sequence in the CP genome contained an additional copy each of lrp and brnFE genes, which benefited the export of L-leucine. However, in XV, the kgd and panB genes were disrupted by nucleotide insertion, which increase the availability of precursors to synthesize L-valine. Moreover, the specific amino acid substitutions in key enzymes increased their activities. Additionally, a novel strategy is proposed to remodel central carbon metabolism and reduce pyruvate consumption without having a negative impact on cell growth by introducing the CP-derived mutant $H^+$/citrate symporter. These results further our understanding regarding the metabolic networks in these strains and help to elucidate the influence of different genotypes on these processes.

• Molecules and Cells
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• 제25권4호
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• pp.467-478
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• 2008

Simple sequence repeats (SSRs) and interSSR (ISSR) marker systems were used in this study to reveal genetic changes induced by artificial selection for short/long larval duration in the tropical strain Nistari of the silkworm Bombyx mori. Artificial selection separated longer larval duration (LLD) ($29.428{\pm}0.723days$) and shorter larval duration (SLD) ($22.573{\pm}0.839days$) lines from a base, inbred population of Nistari (larval span of $23.143{\pm}0.35days$). SSR polymorphism was observed between the LLD and SLD lines at one microsatellite locus, Bmsat106 ($CA_7$) and at two loci of 1074 bp and 823 bp generated with the ISSR primer UBC873. Each of these loci was present only in the LLD line. The loci segregated in the third generation of selection and were fixed in opposite directions. In the $F_2$ generation of the $LLD{\times}SLD$ lines, the alleles of Bmsat106 and $UBC873_{1074bp}$ segregated in a 1:1 ratio and the loci were present only in the LLD individuals. $UBC873_{823bp}$ was homozygous. Single factor ANOVA showed a significant association between the segregating loci and longer larval duration. Together, the two alleles contributed to an 18% increase in larval duration. The nucleotide sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci had 67% A/T content and consisted of direct, reverse, complementary and palindromic repeats. The repeats appeared to be "nested" (59%) in larger repeats or as clustered elements adjacent to other repeats. Of 203 microsatellites identified, dinucleotides (67.8%) predominated and were rich in A/T and T/A motifs. The sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci showed similarity (E = 0.0) to contigs located in Scaffold 010774 and Scaffold 000139, respectively, of the B. mori genome. BLASTN analysis of the $UBC873_{1074bp}$ sequence showed significant homology of (nt.) 45-122 with upstream region of three exons from Bombyx. The complete sequence of this locus showed ~49% nucleotide conservation with transposon 412 of Drosophila melanogaster and the Ikirara insertions of Anopheles gambiae. The A + T richness and lack of coding potential of these small loci, and their absence in the SLD line, reflect the active process of genetic change associated with the switch to short larval duration as an adaptation to the tropics.

• 한국패류학회지
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• 제24권1호
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• pp.73-80
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• 2008

동양달팽이의 metallothionein 유전자는 염기서열 195개로 이루어져 있으며 65개의 아미노산으로 이루어져 있었다. 연체동물의 metallothionein 서열의 공식인 C-x-C-x (3) -C-T-G-x (3) -C-x-C-x (3) -C-x-C-K에 맞춰본 결과 알려진 공식과 일치하는 것을 확인할 수 있었으며 아미노산의 조성도 시스테인 (Cys) 이 30% 이상 함유하는 사실을 확인 할 수 있었다. BLAST 결과를 토대로 선정된 72개의 참고 서열 중 아미노산 레벨에서 가장 높은 스코어로 align 되는 서열은 Helix pomatia의 CD-MT 서열이었다. Clustalx를 통해 multiple align 한 후 Neighbor-Joining method 방법에 따라 phylodendrogram을 그려본 결과 Helix pomatia, Helix aspersa, Arianta arbustorum, Megathura crenulata 등과 같은 복족류 육산패들과 같은 그룹으로 묶여지는 것을 확인 할 수 있었다. Psipred 소프트웨어를 통해 2D 구조를 비교 분석 한 결과도 multiplealignment 및 phylodendrogram와 밀접한 관계가 있음을 알 수 있었다. 이러한 결과를 통해 EST를 통해 밝혀진 동양달팽이의 MT서열은 근연종들과 매우 일치함을 알 수 있었으며 MT 서열이 분류에 사용 될 수 있음을 확인시켜 주었다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권8호
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• pp.1183-1189
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• 2017

Objective: Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods: Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2) gene. Subsequently, SH3RF2 was knocked out using clustered regularly interspaced short palindromic repeat/Cas9 technology and single cell-derived SH3RF2 mutant sublines were established to study the biofunctional activity of SH3RF2 in quail myoblast (QM7) cells during muscle differentiation. Results: Through a T7 endonuclease I assay and genotyping analysis, we established an SH3RF2 knockout (KO) QM7#4 subline with 61 and 155 nucleotide deletion mutations in SH3RF2. After the induction of myotube differentiation, the expression profiles were analyzed and compared between regular QM7 and SH3RF2 KO QM7#4 cells by global RNA sequencing and bioinformatics analysis. Conclusion: We did not detect any statistically significant role of SH3RF2 during myotube differentiation in QM7 myoblast cells. However, additional experiments are necessary to examine the biofunctional activity of SH3RF2 in cell proliferation and muscle growth.

• 한국정보과학회논문지:시스템및이론
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• 제33권6호
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• pp.316-325
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• 2006

인간과 같은 2배체의 각 염색체는 부모로부터 물려받은 2벌의 복제로 이루어져 있다. 이들 각 복제에서 SNP(single nucleotide polymorphism) 서열 정보를 하플로타입이라 부른다. 인간의 하플로타입 지도를 완전히 찾는 것은 인간 지놈의 중요한 작업 중의 하나인데, 실험적인 방법으로 하플로타입을 직접 얻는 것은 시간이 많이 걸리고 비용이 많이 든다. 따라서 두 하플로타입 정보가 혼합된 지노타입의 샘플들로부터 하플로타입을 추론하는 것에 대하여 연구되어왔다. 이 논문에서는 지노타입들을 설명하는 최소 개수의 하플로타입들을 찾는 모델(최소 하플로타입 추론문제)에 근거하여, 유전자 알고리즘을 사용하여 하플로타입을 추론하는 새로운 접근 방법을 제시한다. 좋은 결과를 주는 것으로 알려진 HAPAR[1]와 이 논문에 제시한 알고리즘을 컴퓨터 실험에 의한 비교를 통하여, 입력이 클 때 이 논문의 알고리즘이 수행시간은 적게 걸리면서 정확성이 비슷함을 보인다. 또한 이 실험 결과를 최근에 제시된 방법인 PTG[2]와 비교한다.