• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• Archives of Pharmacal Research
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• v.19 no.6
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• pp.497-501
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• 1996

A gene coding for triosephosphate isomerase (TPI) from a rat skeletal muscle cDNA library was cloned and its nucleotide sequence was determined. The 1, 348-bp cDNA clone contains 24 bp $5^I$ noncoding region, the entire 750 bp coding region corresponding to a protein of 249 amino acids, $547bp 3^I$ noncoding region and part of a poly(A) tail. It also contains a polyadenylation signal, AATAAA, starting from 17 bp upstream of the poly(A) tail. The calculated molecular weight of rat TPI is 27.8 kDa and the net charge is +4. The deduced amino acid sequence from rat TPI CDNA sequence has 93% and 94% homology with that of mouse and human clones, respectively. The amino acids at the residue of Asn12, Lys14, His96, Glu 166, His96, His101, Ala177, Tyr165, Glu13O, Tyr2O9, and Ser212 in catalytic site are completely identical, confirming that the functional residues in TPI proteins are highly conserved throughout evolution. The most profound characteristic of rat TPI enzyme, compared with other TPIs, is that there are five cysteine substitutions at the residue of 21, 27, 159, 195 and 204. A Glu123 instead of Gly was found in rabbit, rhesus, mouse and human sequences. Through the method of RT-PCR, the mRNA transcription level of TPI gene was found to be different among various tissues and was highest in muscle.

• Journal of Plant Biotechnology
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• v.40 no.1
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• pp.27-36
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• 2013

We isolated and functionally characterized a Dendrobium Actin1 (DmACT1) promoter that drives strong gene expression in the orchid genus Dendrobium. A genomic fragment containing the region 3227 bp upstream of the coding region of DmACT1 was obtained by inverse PCR. Detailed comparison of the full-length cDNA and genomic sequences revealed that DmACT1 has a 1374 bp first intron in the 5' UTR. However, the 5' flanking sequences upstream of the coding region showed no obvious sequence similarities compared to those of known promoters, including plant actin promoters. Serial deletion constructs of the 5' flanking region from the translation initiation codon were fused to the coding sequence of a GUS/luciferase fusion reporter to identify the regulatory elements necessary for promoter activity. Transient assays in the flowers of Dendrobium revealed that the 5' UTR-intron greatly enhanced promoter activity. Moreover, the DmACT1 promoter with its 5' UTR-intron yielded approximately 10-fold higher reporter activity than the rice Act1 promoter-intron. Our data suggest that the DmACT1 promoter with its 5' UTR-intron is a useful tool for strong expression of transgenes in Dendrobium orchids.

• Molecules and Cells
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• v.26 no.5
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• pp.474-480
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• 2008

OsMADS1 is a rice MADS box gene necessary for floral development. To identify the key cis-regulatory regions for its expression, we utilized transgenic rice plants expressing GUS fusion constructs. Histochemical analysis revealed that the 5.7-kb OsMADS1 intragenic sequences, encompassing exon 1, intron 1, and a part of exon 2, together with the 1.9-kb 5' upstream promoter region, are required for the GUS expression pattern that coincides with flower-preferential expression of OsMADS1. In contrast, the 5' upstream promoter sequence lacking this intragenic region caused ectopic expression of the reporter gene in both vegetative and reproductive tissues. Notably, incorporation of the intragenic region into the CaMV35S promoter directed the GUS expression pattern similar to that of the endogenous spatial expression of OsMADS1 in flowers. In addition, our transient gene expression assay revealed that the large first intron following the CaMV35S minimal promoter enhances flower-preferential expression of GUS. These results suggest that the OsMADS1 intragenic sequence, largely intron 1, contains a key regulatory region(s) essential for expression.

• Molecules and Cells
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• v.27 no.3
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Korean Journal of Microbiology
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• v.43 no.2
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• pp.111-115
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• 2007

The aim of this study was to isolate and identify men fungus which produces conjugated linoleic acid. IS-13 fungus hydrogenated conjugated linoleic acid and trans-11 vaccenic acid within 12 hr after addition of linoleic acid. The homology of IS-13 rumen fungus was compared with internal transcribed spacer 1 region (ITS1)sequences of twenty three men fungi. The length of ITS1 region of IS-13 isolate was 218 bp. IS-13 isolate has the most similar sequence (98% matched) with Orpinomyces species according to maximum-likehood and distance matrix results. The result supported that IS-13 isolate belonged to Orpinomyces genus.

• The Plant Pathology Journal
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• v.21 no.1
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• pp.27-32
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• 2005

Leaf anthracnose was observed on leaves of Japanese spindle tree in Seoul, Korea from autumn 2003 to spring 2004. The causal fungus was purely isolated from he leaf spot lesions and cultured on PDA. The colony on PDA was cream to orange but blackish in the center n old cultures. Conidia were formed in blackish orange asses and were cylindrical in shape, measured 13-17${\times}$5-7 ${\mu}$m in size. Blackish brown setae were often observed on PDA and ranged up to 100 ${\mu}$m in length. Based on morphological and ITS region sequence analyses, the fungal strain was identified as Colletotrichum boninense. Koch’s postulates were fulfilled by inoculating tree leaves with 1 ${\times}$ $106^6$ conidia per ml in a moist chamber. This is the first study on the pathogenicity, growth and phylogenetic characteristics of C. boninense causing leaf anthracnose on Japanese spindle tree in Korea.

• Journal of Life Science
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• v.22 no.1
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• pp.62-73
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• 2012

This study was carried out to investigate the genetic relationship of Flammulina velutipes with other species. The ribosomal DNA cluster containing 4 rRNA genes from F. velutipes 4154 were sequenced. The length of the rDNA cluster sequence was estimated at 7,403 bp long and consisted of 1,806 bp of SSU rDNA, 245 bp of ITS 1 region, 159 bp of 5.8S rDNA, 308 bp of ITS 2 region, 3,402 bp of LSU rDNA, 1,400 bp of IGS 1 region, and 83 bp of 5S rDNA. The F. velutipes 4154 genes were contained in the rDNA cluster of F. velutipes in the order of SSU rDNA - ITS 1 - 5.8S rDNA - ITS 2 - LSU rDNA - IGS 1 - 5S rDNA. The phylogenetic relationships of 20 strains of Tricholomataceae and Physalacriaceae were analyzed by conducting distance analysis using the Neighbor-joining (NJ) method. The 20 strains used in this study were divided into three groups and the strains of the genus Flammulina were related very closely to strains of Physalacria bambusae.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.43-43
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• 2018

Dumortiera hirsuta (Sw.) Nees (Dumortieraceae) is a thallose liverwort distributed in tropics and subtropics. It is the only species in family Dumortieraceae, which is the second basal family in order Marchantiales. D. hirsuta is characterized by hairy receptacles and lacking air chamber. The complete chloroplast genome of D. hirsuta was successfully rescued from raw reads generated by HiSeq4000. Its total length is 122,050 bp consisting of four regions: large single copy (LSC) region (81,697 bp), small single copy (SSC) region (20,061 bp), and two inverted repeats (IRs; 10,146 bp per each). It contained 129 genes (84 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes including four rRNAs, and five tRNAs are duplicated in the IR regions. The overall GC content of D. hirsuta is 28.7%, which is almost same to that of Marchantia paleacea. Phylogenetic tree based on all genes from whole chloroplast genomes will provides phylogenetic position of D. hirstua. This sequence will be an fundamental resources for further researches of order Marchantiales.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.69-70
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• 2000

The completion of sequencing human genome would motivate us to map millions of human cDNAs onto the unique ruler "genome sequence", in order to identify the exact address of each cDNA together with its exons, its promoter region, and its alternative splicing patterns. The expression patterns of some cDNAs could therefore be associated with these precise gene addresses, which further accelerate studies on mining correlations between motifs of promoters and expressions of genes in tissues. Towards the realization of this goal, we have developed a time-and-space efficient software named SQUALL that is able to map one cDNA sequence of length a few thousand onto a long genome sequence of length thirty million in a couple of minutes on average. Using SQUALL, we have mapped twenty thousand of our Bodymap (http://bodymap.ims.u-tokyo.ac.jp) cDNAs onto the genome sequences of Chr.21st and 22nd. In this talk, I will report the status of this ongoing project.