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조연화,최호성,Miah Bae,김상민,김선림,이봉춘,조원경,김국형 한국식물병리학회 2017 Plant Pathology Journal Vol.33 No.5
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
조연화,최호성,홍진성,정현정,최수연,김상민,이봉춘,조원경 한국미생물학회 2022 미생물학회지 Vol.58 No.3
To identify viruses infecting peanut (Arachis hypogaea L.) plants, we collected leaf samples from three peanut plants showing viral disease symptoms in Jeonju, Korea. After extracting total RNA from the individual plant samples, we generated three different ribosome-deleted libraries for RNAsequencing. The three libraries were paired-end sequenced, and the raw data were used for de novo transcriptome assembly followed by a BLASTN search against a viral genome database. We only identified bean common mosaic virus (BCMV) infecting all three peanut plants. From the three libraries, we obtained three complete genomes of BCMV 10,049 nucleotides to 10,039 nucleotides in length encoding two open reading frames. All three BCMV complete genomes showed sequence similarity to the known BCMV isolate Habin1 identified from soybean in Korea. This result suggests that BCMV infecting peanut might originate from BCMV infecting soybean or vice versa. Taken together, we report complete genome sequences of three BCMV isolates identified from peanut in Korea.
조연화,박서연,나종문,김태웅,이주헌 한국습지학회 2019 한국습지학회지 Vol.21 No.5
Alteration in the flow regime of rivers are caused by natural climate change and the changes in anthropogenic hydrological environment due to dam construction. These changes in flow regime cause serious changes not only in the fresh water ecosystems of the rivers but also in the physical structures and fish habitats of the streams. In this study, the alteration in the hydrological characteristics of the Gam river basin due to Buhang dam construction and the changes in ecological health condition, water quality, and river cross-section were analyzed. As a result of analysis by indicators of hydrologic alteration (IHA) to quantitatively change the flow regime of Gam river, HA (Hydrologic Alteration) is more than ± 1 and various changes have occurred in the river ecosystem after Buhang dam construction. In addition, ecological health condition and water quality showed different response for each element, and in the case of riverbeds and channel cross-sections, the degradation of channel bed was obviously monitored after dam construction. The results of this study are expected to be used as an efficient method for evaluating changes in stream ecosystems caused by stream regime changes. 자연적 기후변화와 댐 건설로 인한 인위적 수문환경의 변화로 인하여 하천의 유황(flow regime) 변화가 발생하며, 이러한 유황의 변화는 하천의 생태계뿐만 아니라 하천의 물리적 구조와 어류서식처 등에도 심각한 변화를 야기한다. 본 연구에서는 감천유역의 부항댐 건설로 인하여 나타난 수문특성변화와 동시에 하천의 생태건강성 및 수질, 하천단면 변화를 분석하였다. 감천의 유황 변화를 정량적으로 파악하기 위해 수문변화지표(Indicators of Hydrologic Alteration, IHA)에 의한 분석 결과, HA(Hydrologic Alteration)가 대부분 ±1 이상으로 댐 건설 후 하천생태계에 다양한 변화가 발생한 것으로 판단된다. 또한, 생태건강성등급 및 수질은 각 요소마다 상이한 반응이 나타났으며, 하천의 하상 및 단면의 경우에는, 댐 건설 후에 하상 단면의 저하가 뚜렷하게 나타났다. 본 연구의 성과는 하천의 유황 변화에 의한 하천생태계의 변화를 평가하기 위한 효율적인 방법으로 활용될 수 있을 것으로 기대된다.
조연화,최호성,최수연,김상민,이봉춘,조원경 한국미생물학회 2020 미생물학회지 Vol.56 No.3
To identify viruses infecting soybean (Glycine max L.), we collected soybean leaf samples showing viral disease symptoms and subjected them to RNA-sequencing. De novo transcriptome assembly followed by BLAST search identified Peanut mottle virus (PeMoV) belonging to the genus Potyvirus in the family Potyviridae. We obtained the complete genome of PeMoV isolate Daegu with 9,708 nucleotides encoding polypeptide (3,099 aa) and pretty interesting potyviridae ORF (PIPO) (74 aa) proteins. The phylogenetic analysis using 10 available complete genomes for PeMoV isolates demonstrated that PeMoV isolate Daegu is grouped with five other PeMoV isolates from Korea, China, Kenya, and Brazil.
조연화,Hoseong Choi,Sang-Min Kim,Bong Choon Lee,Won Kyong Cho 한국응용생명화학회 2020 Journal of Applied Biological Chemistry (J. Appl. Vol.63 No.3
The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.
Complete genome sequence of Bean pod mottle virus identified from common bean (Phaseolus vulgaris)
조연화,Hoseong Choi,Soo Yeon Choi,Sang-Min Kim,Yu Mi Choi,Bong-Choon Lee,Won Kyong Cho 한국미생물학회 2020 미생물학회지 Vol.56 No.4
Bean pod mottle virus (BPMV) in the genus Comovirus is a plant virus infecting common bean. We obtained genomes of two BPMV isolates referred as Tigerskin-A and Tigerskin-B consisting of two RNA segments from common bean plants displaying viral disease symptoms by RNA-sequencing. RNA1 encodes a single polyprotein containing five mature proteins while RNA2 encodes a single polyprotein containing a movement protein and two coat proteins. The two BPMV isolates showed high sequence similarity (99.65% to 99.70%) to two isolates, IA-Di1 and Iowa-Desmodium illinoense 1, from the Desmodium illinoense in USA belonging to a flowering plant in the bean family.
조연화(Yeon Hwa Cho),이규정(Kyu Jung Lee),문동주(Dong Ju Moon),김윤호(Yoon Ho Kim) 대한기계학회 2010 대한기계학회 춘추학술대회 Vol.2010 No.5
새롭게 제안된 형상의 마이크로채널 PCHE는 기존의 상용 열교환기에 비해 고성능, 고효율의 특성을 보이며 열교환을 수행한다. 본 연구에서는 I, Wavy, Beehive, Surf, I-Wavy, I-Beehive, I-Surf의 형상을 갖는 다양한 마이크로채널을 모델링하였다. 질량유속 변화에 따른 다양한 마이크로채널 내 유체의 유동 특성, 열전달, 압력강하를 살펴보았고 그 결과는 마이크로채널의 열전달 능력을 향상시키는데 향상시키는데 이용된다. I 채널은 새롭게 적용된 채널 형상과의 성능비교를 위해 해석을 수행하였다. 다양한 레이놀즈수 변화 하에서 고온측과 저온측 유체는 대향류 형태로 열교환이 이루어지도록 하였다. 수치해석 결과 Surf 형상이 다른 형상들보다 열교환 성능이 우수함을 확인하였다. The microchannel PCHE(printed Circuit Heat Exchanger) of the newly proposed shapes out-performs other existing commercial heat exchangers while retaining greater performance-effectiveness and energy-efficiency. Various microchannels with the shapes of I, Wavy, Beehive, Surf, I-Wavy, I-Beehive and I-Surf are computationally modeled in this study. Flow characteristics, heat transfer and pressure drop in the microchannel are investigated under the various mass flow rate conditions. The results are utilized to enhance the heat transfer performance of the microchannels. The I microchannel case is chosen to be benchmark case, whose results are compared with those of newly proposed microchannels. The counterflow is arranged at various Reynolds numbers of both hot and cold fluids. It is found that the shapes of surf is better than the others from the point of heat performance.