• Journal of Microbiology and Biotechnology
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• v.25 no.5
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• pp.606-611
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• 2015

As Salmonella enterica serovar Pullorum remains a major economic problem for the poultry industries of countries with no efficient control measures, we presented a multidrug resistance strain S06004 (isolated from a clinically sick chicken in China in 2006) for genome sequencing. The genome comparison showed that the strain contained two prophages, the ST104 and prophage-4 (Fels2) of E. coli LF82, which were not detected in the only published genomes of S. Pullorum RKS5078 and CDC1983-67. In addition, the GyrA Ser83 point mutation, drugresistant genes, and many antibiotic pump systems that are present in S06004 may be contributing to the multidrug resistance of this strain.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.135-135
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• 2017

The Gramene database (http://www.gramene.org) is a powerful online resource for agricultural researchers, plant breeders and educators that provides easy access to reference data, visualizations and analytical tools for conducting cross-species comparisons. Learn the benefits of using Gramene to enrich your lectures, accelerate your research goals, and respond to your organismal community needs. Gramene's genomes portal hosts browsers for 44 complete reference genomes, including crops and model organisms, each displaying functional annotations, gene-trees with orthologous and paralogous gene classification, and whole-genome alignments. SNP and structural diversity data, available for 11 species, are displayed in the context of gene annotation, protein domains and functional consequences on transcript structure (e.g., missense variant). Browsers from multiple species can be viewed simultaneously with links to community-driven organismal databases. Thus, while hosting the underlying data for comparative studies, the portal also provides unified access to diverse plant community resources, and the ability for communities to upload and display private data sets in multiple standard formats. Our BioMart data mining interface enable complex queries and bulk download of sequence, annotation, homology and variation data. Gramene's pathway portal, the Plant Reactome, hosts over 240 pathways curated in rice and inferred in 66 additional plant species by orthology projection. Users may compare pathways across species, query and visualize curated expression data from EMBL-EBI's Expression Atlas in the context of pathways, analyze genome-scale expression data, and conduct pathway enrichment analysis. Our integrated search database and modern user interface leverage these diverse annotations to facilitate finding genes through selecting auto-suggested filters with interactive views of the results.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.536-557
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• 2020

Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.309-312
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• 2019

Comamonas sp. NLF-7-7 was isolated from biofilter of wastewater treatment plant. The whole-genome sequence of Comamonas sp. NLF-7-7 was analyzed using the PacBio RS II and Illumina HiSeqXten platform. The genome comprises a 3,333,437 bp chromosome with a G + C content of 68.04%, 3,197 total genes, 9 rRNA genes, and 49 tRNA genes. This genome contained pollutants degradation and floc forming genes such as sulfur oxidization pathway (SoxY, SoxZ, SoxA, and SoxB) and floc forming pathway (EpsG, EpsE, EpsF, EpsG, EpsL, and glycosyltransferase), respectively. The Comamonas sp. NLF-7-7 can be used to the purification of wastewater.

• Journal of Plant Biotechnology
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• v.48 no.1
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• pp.18-25
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• 2021

Solanum demissum is one of the wild Solanum species originating from Mexico. It has wildly been used for potato breeding due to its resistance to Phytophthora infestans. S. demissum has an EBN value of four, which is same as that of S. tuberosum, so that it is directly crossable for breeding purposes with the cultivated tetraploid potato (S. tuberosum). In this study, the chloroplast genome sequence of S. demissum obtained by next-generation sequencing technology was described and compared with those of seven other Solanum species to develop S. demissum-specific markers. Thetotal sequence length of the chloroplast genome is 155,558 bp, and its structural organization is similar to those of other Solanum species. Phylogenetic analysis with ten other Solanaceae species revealed that S. demissum is most closely grouped with S. hougasii and S. stoloniferum followed by S. berthaultii and S. tuberosum. Additional comparison of the chloroplast genome sequence with those of seven other Solanum species revealed two InDels specific to S. demissum. Based on these InDels, two PCR-based markers for discriminating S. demissum from other Solanum species were developed. The results obtained in this study will provide an opportunity to investigate more detailed evolutionary and breeding aspects in Solanum species.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.30-38
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• 2022

Solanum brevicaule is one of the tuber-bearing wild Solanum species. Because of its resistance to several important pathogens infecting potatoes during cultivation, it can be used for potato breeding. However, the fact that S. brevicaule used in this study has an EBN value of two causes the sexual reproduction barriers between the species and cultivated potatoes. In this study, specific markers for discriminating S. brevicaule from other Solanum species were developed on the basis of the results of sequence alignments with the whole chloroplast genomes of S. brevicaule and seven other Solanum species. The chloroplast genome of S. brevicaule was completed by next-generation sequencing technology described in other recent studies. The total sequence length of the chloroplast genome of S. brevicaule is 155,531 bp. Its structure and gene composition are similar to those of other Solanum species. Phylogenetic analysis revealed that S. brevicaule was closely grouped with other Solanum species. BLASTN search showed that its genome sequence had 99.99% and 99.89% identity with those of S. spegazzinii (MH021562) and S. kurtzianum (MH021495), respectively. Sequence alignment identified 27 SNPs that were specific to S. brevicaule. Thus, three PCR-based CAPS markers specific to S. brevicaule were developed on the basis of these SNPs. This study will facilitate in further studies on evolutionary and breeding aspects in Solanum species.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.2
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• pp.69-75
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• 2004

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional I protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4229-4233
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• 2012

With the advances in modern diagnostic expertise for cancer, certain approaches allowing scanning of the complete genome and the proteome are becoming very useful for researchers. These high throughput techniques have already proven power, over traditional detection methods, in differentiating disease sub-types and identifying specific genetic events during progression of cancer. This paper introduces major branches of omics-technology and their applications in the field of cancer. It also addresses current road blocks that need to be overcome and future possibilities of these methods in oncogenic detection.

• Proceedings of the Korean Society of Applied Entomolohy Conference
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• 2001.11a
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• pp.130-130
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• 2001

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.141-141
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• 2005