• Journal of Animal Science and Technology
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• v.65 no.2
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• pp.473-477
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• 2023

Lactobacillus amylovorus CACC736 was originated from swine feces in Korea. The complete genome sequences of the strain contained one circular chromosome (2,057,809 base pair [bp]) with 38.2% guanine-cytosine (GC) content and two circular plasmids, namely, pCACC736-1 and pCACC736-2. The predicted protein-coding genes, which are encoding the clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins, biosynthesis of bacteriocin (helveticin J), and the related proteins of the bile, acid tolerance. Notably, the genes related to vitamin B-group biosynthesis (riboflavin and cobalamin) were also found in L. amylovorus CACC736. Collectively, the complete genome sequence of the L. amylovorus CACC736 will aid in the development of functional probiotics in the animal industry.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Genomics & Informatics
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• v.19 no.1
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• pp.2.1-2.10
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• 2021

BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.468-475
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• 2020

Malva vein clearing virus (MVCV) is a member of the Potyvirus species, and has a negative impact on the aesthetic development of Alcea rosea. It was first reported in Germany in 1957, but its complete genome sequence data are still scarce. In the present work, A. rosea leaves with vein-clearing and mosaic symptoms were sampled and analyzed with small RNA deep sequencing. By denovo assembly the raw sequences of virus-derived small interfering RNAs (vsiRs) and whole genome amplification of malva vein cleaning virus SX strain (MVCV-SX) by specific primers targeting identified contig gaps, the full-length genome sequences (9,645 nucleotides) of MVCV-SX were characterized, constituting of an open reading frame that is long enough to encode 3,096 amino acids. Phylogenetic analysis showed that MVCV-SX was clustered with euphorbia ringspot virus and yam mosaic virus. Further analyses of the vsiR profiles revealed that the most abundant MVCV-vsiRs were between 21 and 22 nucleotides in length and a strong bias was found for "A" and "U" at the 5′-terminal residue. The results of polarity assessment indicated that the amount of sense strand was almost equal to that of the antisense strand in MVCV-vsiRs, and the main hot-spot region in MVCV-SX genome was found at cylindrical inclusion. In conclusion, our findings could provide new insights into the RNA silencing-mediated host defence mechanism in A. rosea infected with MVCV-SX, and offer a basis for the prevention and treatment of this virus disease.

• Journal of Animal Science and Technology
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• v.63 no.5
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• pp.1207-1210
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• 2021

Lactobacillus amylovorus are known to exist in the intestinal flora of healthy cattle or pigs. The L. amylovorus strain 1394N20 was isolated from the feces of the Hanwoo calf (Bos taurus coreanae). The genome of strain 1394N20 consists of a single circular chromosome (2,176,326 bp) with overall guanine + cytosine content of 37.8 mol%. Moreover, 2,281 protein-coding sequences, 15 rRNAs, and 65 tRNAs genes were identified in the chromosome based on the results of annotation. The bacterium has a gene encoding endoglucanase, an enzyme that hydrolyzes the 1,4-β-D-glycosidic linkages in cellulose, hemicellulose, lichenin, and cereal β-D-glucans. Genomic sequencing of L. amylovorus strain 1394N20 reveals the immense potential of the strain as a probiotic with nutrient digestibility.

• Molecules and Cells
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• v.43 no.1
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• pp.86-95
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• 2020

The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH, RPA1, PHAX, HNMT, HS2ST1, PPCDC, PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.12-20
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• 2016

Advances in DNA sequencing technologies have contributed to revolutionary understanding of many fundamental biological processes. With unprecedented cost-effective and high-throughput sequencing, a single laboratory can afford to de novo sequence the whole genome for species of interest. In addition, population genetic studies have been remarkably accelerated by numerous molecular markers identified from unbiased genome-wide sequences of population samples. As sequencing technologies have evolved very rapidly, acquiring appropriate individual plants or populations is a major bottleneck in plant research considering the complex nature of plant genome, such as heterozygosity, repetitiveness, and polyploidy. This challenge could be overcome by the old but effective method known as haploid induction. Haploid plants containing half of their sporophytic chromosomes can be rapidly generated mainly by culturing gametophytic cells such as ovules or pollens. Subsequent chromosome doubling in haploid plants can generate stable doubled haploid (DH) with perfect homozygosity. Here, classical methodology to generate and identify haploid plants or DH are summarized. In addition, haploid induction by epigenetic regulation of centromeric histone is explained. Furthermore, the utilization of haploid plant in the genomics era is discussed in the aspect of genome sequencing project and population genetic studies.

• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.411-416
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• 2016

Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions absent in the reference cannot be identified by simple alignment. In this review, we report the current status and prospects in identification of genes in mutant phenotypes, by using the methods MutMap, MutMap-Gap, and MutMap+. These methods delineate a candidate region harboring a mutation of interest, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. These methods are likely to prove useful for cloning genes that exhibit significant structural variations, such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.12
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• pp.1980-1990
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• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• Research in Plant Disease
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• v.29 no.3
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• pp.321-329
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• 2023

The bacterium Neobacillus endophyticus BRMEA1^T, isolated from the medicinal plant Selaginella involvens, known as its thermotolerant can grow at 50℃. To explore the genetic basis for its heat tolerance response and its potential for producing valuable natural compounds, the genomes of two thermotolerant and four mesophilic strains in the genus Neobacillus were analyzed using a bioinformatic software platform. The whole genome was annotated using RAST SEED and OrthVenn2, with a focus on identifying potential heattolerance-related genes. N. endophyticus BRMEA1^T was found to possess more stress response genes compared to other mesophilic members of the genus, and it was the only strain that had genes for the synthesis of osmoregulated periplasmic glucans. This study sheds light on the potential value of N. endophyticus BRMEA1^T, as it reveals the mechanism of heat resistance and the application of secondary metabolites produced by this bacterium through whole-genome sequencing and comparative analysis.