• Journal of Plant Biotechnology
• /
• v.41 no.1
• /
• pp.26-32
• /
• 2014

Recent genome annotation revealed that Populus trichocarpa contains 81 glutathione S-transferase (GST) genes. GST genes play important and varying roles in plants, including conferring tolerance to various abiotic stresses. Little information is available on the relationship - if any - between drought/salt stresses and GSTs in woody plants. In this study, we screened the PatgGST genes in hybrid poplar (Populus alba ${\times}$ Populus tremula var. glandulosa) that were predicted to confer drought tolerance based on our expression analysis of all members of the poplar GST superfamily following exposure to salt (NaCl) and drought (PEG) stresses, respectively. Exposure to the salt stress resulted in the induction of eight PatgGST genes and down-regulation of one PatgGST gene, and the level of induction/repression was different in leaf and stem tissues. In contrast, 16 PatgGST genes were induced following exposure to the drought (PEG) stress, and two were down-regulated. Taken together, we identified seven PatgGSTs (PatgGSTU15, PatgGSTU18, PatgGSTU22, PatgGSTU27, PatgGSTU46, PatgGSTU51 and PatgGSTU52) as putative drought tolerance genes based on their induction by both salt and drought stresses.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.2
• /
• pp.290-296
• /
• 2019

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. Methods: nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Results: The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. Conclusion: The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.

• Animal Bioscience
• /
• v.35 no.11
• /
• pp.1656-1665
• /
• 2022

Objective: Water buffalo, an important domestic animal in tropical and subtropical regions, play an important role in agricultural economy. It is an important source for milk, meat, horns, skin, and draft power, especially its rich milk that is the great source of cream, butter, yogurt, and many cheeses. In recent years, long noncoding RNAs (lncRNAs) have been reported to play pivotal roles in many biological processes. Previous studies for the mammary gland development of water buffalo mainly focus on protein coding genes. However, lncRNAs of water buffalo remain poorly understood, and the regulation relationship between mammary gland development/milk production traits and lncRNA expression is also unclear. Methods: Here, we sequenced 22 samples of the milk somatic cells from three lactation stages and integrated the current annotation and identified 7,962 lncRNA genes. Results: By comparing the lncRNA genes of the water buffalo in the early, peak, and late different lactation stages, we found that lncRNA gene lnc-bbug14207 displayed significantly different expression between early and late lactation stages. And lnc-bbug14207 may regulate neighboring milk fat globule-EGF factor 8 (MFG-E8) and hyaluronan and proteoglycan link protein 3 (HAPLN3) protein coding genes, which are vital for mammary gland development. Conclusion: This study provides the first genome-wide identification of water buffalo lncRNAs and unveils the potential lncRNAs that impact mammary gland development.

• Microbiology and Biotechnology Letters
• /
• v.50 no.4
• /
• pp.563-573
• /
• 2022

Xanthomonas arboricola pv. juglandis (Xaj) is a globally important bacterial pathogen of walnut trees that causes substantial economic losses in commercial walnut production. Although prophages are common in bacterial plant pathogens and play important roles in bacterial diversity and pathogenicity, there has been limited investigation into the distribution and function of prophages in Xaj. In this study, we identified and characterized 13 predicted prophages from the genomes of 12 Xaj isolates from around the globe. These prophages ranged in length from 11.8 kb to 51.9 kb, with between 11-75 genes and 57.82-64.15% GC content. The closest relatives of these prophages belong to the Myoviridae and Siphoviridae families of the Caudovirales order. The phylogenetic analysis allowed the classification of the prophages into five groups. The gene constitution of these predicted prophages was revealed via Roary analysis. Amongst 126 total protein groups, the most prevalent group was only present in nine prophages, and 22 protein groups were present in only one prophage (singletons). Also, bioinformatic analysis of the 13 identified prophages revealed the presence of 431 genes with an average length of 389.7 bp. Prokka annotation of these prophages identified 466 hypothetical proteins, 24 proteins with known function, and six tRNA genes. The proteins with known function mainly comprised prophage integrase IntA, replicative DNA helicase, tyrosine recombinase XerC, and IS3 family transposase. There was no detectable insertion site specificity for these prophages in the Xaj genomes. The identified Xaj prophage genes, particularly those of unknown function, merit future investigation.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.5
• /
• pp.644-655
• /
• 2023

Safety assessment and functional analysis of probiotic candidates are important for their industrial applications. Lactiplantibacillus plantarum is one of the most widely recognized probiotic strains. In this study we aimed to determine the functional genes of L. plantarum LRCC5310, isolated from kimchi, using next-generation, whole-genome sequencing analysis. Genes were annotated using the Rapid Annotations using Subsystems Technology (RAST) server and the National Center for Biotechnology Information (NCBI) pipelines to establish the strain's probiotic potential. Phylogenetic analysis of L. plantarum LRCC5310 and related strains showed that LRCC5310 belonged to L. plantarum. However, comparative analysis revealed genetic differences between L. plantarum strains. Carbon metabolic pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that L. plantarum LRCC5310 is a homofermentative bacterium. Furthermore, gene annotation results indicated that the L. plantarum LRCC5310 genome encodes an almost complete vitamin B₆ biosynthetic pathway. Among five L. plantarum strains, including L. plantarum ATCC 14917^T , L. plantarum LRCC5310 detected the highest concentration of pyridoxal 5'-phosphate with 88.08 ± 0.67 nM in MRS broth. These results indicated that L. plantarum LRCC5310 could be used as a functional probiotic for vitamin B₆ supplementation.

• Animal Bioscience
• /
• v.36 no.9
• /
• pp.1367-1375
• /
• 2023

Objective: Pigment production and distribution are controlled through multiple proteins, resulting in different coat color phenotypes of sheep. Methods: The expression distribution of vimentin (VIM) and transthyretin (TTR) in white and black sheep skins was detected by liquid chromatography-electrospray ionization tandem MS (LC-ESI-MS/MS), gene ontology (GO) statistics, immunohistochemistry, Western blot, and quantitative real time polymerase chain reaction (qRT-PCR) to evaluate their role in the coat color formation of sheep. Results: LC-ESI-MS/MS results showed VIM and TTR proteins in white and black skin tissues of sheep. Meanwhile, GO functional annotation analysis suggested that VIM and TTR proteins were mainly concentrated in cellular components and biological process, respectively. Further research confirmed that VIM and TTR proteins were expressed at significantly higher levels in black sheep skins than in white sheep skins by Western blot, respectively. Immunohistochemistry notably detected VIM and TTR in hair follicle, dermal papilla, and outer root sheath of white and black sheep skins. qRT-PCR results also revealed that the expression of VIM and TTR mRNAs was higher in black sheep skins than in white sheep skins. Conclusion: The expression of VIM and TTR were higher in black sheep skins than in white sheep skins and the transcription and translation were unanimous in this study. VIM and TTR proteins were expressed in hair follicles of white and black sheep skins. These results suggested that VIM and TTR were involved in the coat color formation of sheep.

• Genomics & Informatics
• /
• v.21 no.4
• /
• pp.48.1-48.8
• /
• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• Journal of Ecology and Environment
• /
• v.48 no.2
• /
• pp.163-172
• /
• 2024

Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.

• Research in Plant Disease
• /
• v.30 no.3
• /
• pp.268-277
• /
• 2024

Erwinia pyrifoliae is a gram-negative bacterial pathogen that commonly causes black shoot blight in pear and apple tree. Although the pathogenicity of this bacterial species is very similar to E. amylovora, there is no specific explanation of its pathogenic genes and mechanisms. In this study, our investigation into E. pyrifoliae pathogenicity involved generating seven YKB12327 mutant strains using Tn5 transposon mutagenesis. Observations revealed weakened growth rate and loss of pathogenicity in these mutants. Whole-genome sequencing and alignment analysis identified transposon insertions within the coding sequences of five strains and in the intergenic region of two strains. Annotation analysis elucidated genes directly or indirectly associated with pathogenicity. Notably, mutant strain MT16 displayed a transposon insertion mutation in the cyclic-di-GMP phosphodiesterase (pdeF) gene, a key player in bacterial signaling, governing microbial behavior and adaptation to environmental changes. Our findings provide insights into the genetic regulation of E. pyrifoliae pathogenicity, suggesting potential avenues for further research aimed at understanding and controlling this bacterial pathogen by targeting pdeF to mitigate apple black shoot blight disease.

• The Korean Journal of Mycology
• /
• v.47 no.4
• /
• pp.417-425
• /
• 2019

Biocontrol agents (BCAs) are widely used to protect plants from diverse biotic and abiotic stresses in agricultural and ecological fields. Among the various microbes, many subspecies of the gram-positive genus, Bacillus, have been successfully industrialized as eco-friendly biological pesticides and fertilizers. In the current study, we demonstrated that Bacillus thuringiensis C25 exhibited antagonistic effects on the mycelial growth of Rosellinia necatrix, a fungal phytopathogen. Scanning electron microscopy analysis revealed that B. thuringiensis C25 degraded the cell wall structures of R. necatrix mycelia. In the functional genomic analysis of B. thuringiensis C25, we annotated 5,683 genes and selected the gene sets that potentially encoded fungal cell wall degrading enzymes (CWDEs). The growth inhibition effects on R. necatrix were highly correlated with the transcriptional activity of the mycelial cell wall degrading genes of B. thuringiensis C25. The transcript levels of CWDEs, including CshiA, B, and Glycos_transf_2 genes in B. thuringiensis C25, were enhanced following co-cultivation with R. necatrix. In conclusion, our study suggested that B. thuringiensis C25 could serve as a suitable candidate for controlling R. necatrix and could facilitate elucidating the mechanisms underlying the antifungal activities of BCAs against phytopathogens.