• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.547-554
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• 2004

Telomeres are nucleoprotein structures at the ends of chromosomes consisting of tandem repeat sequences of . (TTAGGG)n. Telomeres serve as guardians of the genome, protect individual chromosomes within the nucleus, and help in meiotic pairing of homologous chromosomes. To investigate the telomere distributions of cattle and pig chromosomes, fluorescence in situ hybridization(FISH) was carried out on metaphase spreads of in vitro fibroblast cultures from Holstein and Landrace using a human telomeric DNA repeat probe. Results indicate that the distinct double spots on both ends of chromosomes of cattle and pigs were observed. In cattle, there was a random variation in the intensity of telomere signals among chromosomes. In pigs, an interstitial telomeric signal was observed on the chromosome 6q1 of all the cells examined. According to quantitative fluorescence in situ hybridization(Q-FISH) analysis, some chromosomes had consistently much more telorneres at one end of chromosomes. In general, both species had consistently much more telomeres at q-end than p-end on most of chromosomes. The relative amount of telomeres on bovine chromosomes was higher than that on pig chromosomes. In additions, Y chromosome had the highest relative amount of telorneres in cattle and pigs.

• Mycobiology
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• v.49 no.4
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• pp.406-420
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• 2021

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

• The Korean Journal of Mycology
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• v.37 no.1
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• pp.86-90
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• 2009

The C. militaris belongs to entomopathogenic fungi, which have their specific sequences in internal transcribed spacer regions (ITS1 and ITS2) depending on species. In this study, to identify the phylogenetic relationship of the strain hybrided by mating of C. militaris, we compared DNA sequences of ITS regions and 5.8S ribosomal DNA (rDNA) repeat unit of hybrid strain and its parental strains. The result revealed that hybrid strains are C. militaris species. In addition, cordycepins produced by hybrid strains and other strains of C. militaris were analyzed by HPLC with 20mM $KH_2PO_4$ of mobile phase and C-18 columns. The result indicated that the strain hybrided by mating produce higher concentration of phytochemical cordycepin than other C. militaris strains.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1188-1194
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• 2006

Dementia is a progressive disease of increasing the dysfunction of intellectual and physical ability. In the aging society, many families are suffering from the caring the patients who are diagnosed with dementia. However, dementia is a complex disease affected by the genetic and environmental agents. In the present study, we investigated the transposable elements in relation to dementia. From the analysis of dementia EST (expressed sequence tag) sequences, we found dementia candidate genes, and analyzed expression profiles and repeat elements using bioinformatics tools. This analysis showed that 98 genes were affected in their mRNA sequences by transposable elements expression. Their expressions were affected by the integration of different transposable elements (SINE, LINE, LTR, DNA) during the primate evolution. We believe that our work will be of significant interest to genome scientists, and may help them gain insight into implication of transposable elements expression in dementia.

• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Molecules and Cells
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• v.24 no.3
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• pp.394-408
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• 2007

Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and blb resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.

• Research in Plant Disease
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• v.18 no.4
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• pp.268-276
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• 2012

Broad bean wilt virus 2 (BBWV2), genus Fabavirus, subfamily Comovirinae, family Secoviridae, causes damage in many economically important horticultural and ornamental crops. Sequence alignments showed several conserved sequences in 5' non-coding regions (5' NCRs) of RNA 1 and RNA 2 in all BBWV2 strains characterized so far. Based on this observation, we generated a hpRNA construct (pIR-BBWV2) harboring an inverted repeat containing a 210 bp cDNA fragment homologous to 5' NCR portion of BBWV2 RNA 1 to investigate the silencing potential for its ability to interfere with a rapidly replicating BBWV2. Agrobacterium-mediated transient expression of the IR-BBWV2 had a detrimental effect on BBWV2 infection, showing no distinct symptoms in non-inoculated leaves of the agroinfiltrated Nicotiana benthamiana plants. BBWV2 genomic RNAs were not detected by RT-PCR from tissues of both the inoculated leaves and upper leaves of the agroinfiltrated plants. Accumulation of virus-derived small interfering RNAs was detected in the inoculated leaf tissues of N. benthamiana plants elicited by transient expression of IR-BBWV2 indicating that RNA silencing is responsible for the resistance to BBWV2.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.7
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• pp.1019-1025
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• 2011

Toll-like receptors (TLRs) play an important role in the recognition of invading pathogens and the modulation of innate immune responses in mammals. The TLR4 and TLR7 are well known to recognize the bacterial lipopolysaccharide (LPS) and single stranded (ssRNA) ligands, respectively and play important role in host defense against Gram-negative bacteria and ssRNA viruses. In the present study, coding exon fragments of these two TLRs were identified, cloned, sequenced and analyzed in terms of insertion-deletion polymorphism, within bovine TLRs 4 and 7, thereby facilitating future TLR signaling and association studies relevant to bovine innate immunity. Comparative sequence analysis of TLR 4 exons revealed that this gene is more variable, particularly the coding frame (E3P1), while other parts showed percent identity of 95.7% to 100% at nucleotide and amino acid level, respectivley with other Bos indicus and Bos taurus breeds from different parts of the world. In comparison to TLR4, sequence analysis of TLR7 showed more conservation among different B. indicus and B. taurus breeds, except single point mutation at 324 nucleotide position (AAA to AAM) altering a single amino acid at 108 position (K to X). Percent identity of TLR7 sequences (all 3 exons) was between 99.2% to 100% at nucleotide and amino acid level, when compared with available sequence database of B. indicus and B. taurus. Simple Modular Architecture Research Tool (SMART) analysis showed variations in the exon fragments located in the Leucine Rich Repeat (LRR) region, which is responsible for binding with the microbial associated molecular patterns and further, downstream signaling to initiate anti-microbial response. Considering importance of TLR polymorphism in terms of innate immunity, further research is warranted.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.299-307
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• 2013

A radish (Raphanus sativus L.) polygalacturonase-inhibiting protein (PGIP) gene was cloned and compared to the PGIP gene (BrPGIP2) from Chinese cabbage (Brassica rapa ssp. pekinensis) in order to gain more information on controlling a disease and improving produce quality. To clone the radish PGIP gene, primers were designed based on conserved sequences of two PGIP genes (BnPGIP1 and BnPGIP2) from rape (B. napus L. ssp. oleifera), Chinese cabbage and Arabidopsis thaliana. PCR cloning was performed with cDNA from the stigma of radish 'Daejinyeoreum' as a template to confirm DNA fragments which were about 600 base pair in size. Sequence analysis revealed 84.1% homology with BrPGIP2 and 70.1% with BnPGIP1. DNA walking was conducted to confirm the open reading frame of 972 bp, and the gene was named RsPGIP1. RsPGIP1 consisting with 323 amino acids (aa) has a high leucine content (54/323) and contains 10 leucine-rich repeat domains, as do most BrPGIPs of Chinese cabbage. The gene expression of RsPGIP1 was induced by abiotic stresses and methyl jasmonate. It showed enrichment in the stigma and the primary root than a leaf. Cloning RsPGIP1 will aid to further apply practices on postharvest quality maintenance and disease control of the root.

• Plant Biotechnology Reports
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• v.4 no.2
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• pp.165-172
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• 2010

Genes that are expressed early in specific response to high salinity conditions were isolated from rapeseed plant (Brassica napus L.) using an mRNA differential display method. Five PCR fragments (DD1.5) were isolated that were induced by, but showed different response kinetics to, 200 mM NaCl. Nucleotide sequence analysis and homology search revealed that the deduced amino sequences of three of the five cDNA fragments showed considerable similarity to those of ${\beta}$-mannosidase (DD1), tomato Pti-6 proteins (DD5), and the tobacco harpin-induced protein hin1 (DD4), respectively. In contrast, the remaining clones, DD3 and DD2, did not correspond to any substantial existing annotation. Using the DD3 fragment as a probe, we isolated a full-length cDNA clone from the cDNA library, which we termed BnSWD1 (Brassica napus salt responsive WD40 1). The predicted amino-acid sequence of BnSWD1 contains eight WD40 repeats and is conserved in all eukaryotes. Notably, the BnSWD1 gene is expressed at high levels under salt-stress conditions. Furthermore, we found that BnSWD1 was upregulated after treatment with abscisic acid, salicylic acid, and methyl jasmonate. Our study suggests that BnSWD1, which is a novel WD40 repeat-containing protein, has a function in salt-stress responses in plants, possibly via abscisic acid-dependent and/or -independent signaling pathways.