• Journal of Microbiology and Biotechnology
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• 제12권1호
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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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• 제19권6호
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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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• 제40권1호
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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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• 제26권5호
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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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• 제27권3호
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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.

• 미생물학회지
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• 제43권2호
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• pp.111-115
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• 2007

반추위에서 분리한 곰팡이(IS-13)의 conjugated linoleic acid 생산 과정을 조사하고conjugated linoleic acid를 생산하는 곰팡이를 동정하기 위하여 본 연구를 실시하였다. IS-13 곰팡이가 함유된 배양액에 linoleic acid를 첨가한 결과 linoleic acid는 배양 12시간 이내에 conjugated linoleic acid와 trans-11 vaccenic acid로 biohydrogenation되었다. IS-13 곰팡이의 동정은 internal transcribed spacer 1 영역(ITS1)을 sequence하여 GenBank 유래의 관련 23속(종)의 반추위 곰팡이와 비교하였다. IS-13 곰팡이의 ITS1의 length는 218 bp인 것으로 확인되었으며, 염기서열 분석 결과 Orpinomyces species와 98% 일치하여 반추위내 Orpinomyces species는 conjugated linoleic acid 생산에 깊이 관여하는 것으로 확인되었다. 연구결과 본 균주는 Orpinomyces 속에 속하는 균으로 동정되었다.

• The Plant Pathology Journal
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• 제21권1호
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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.

• 생명과학회지
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• 제22권1호
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• pp.62-73
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• 2012

본 연구는 팽이버섯(Flammulina velutipes)의 국내 균주와 외래 균주간의 유전적 유연관계를 조사하기 위하여 수행되었으며, 계통수 측정 결과 3개 그룹으로 나눠짐을 확인하였다. 20개 F. velutipes 균주들의 ITS region 염기 서열을 확보하였으며, 이들 서열을 바탕으로 multiple alignment를 보았으며, Neighbor-joining method를 이용하여 계통수를 작성하였으며, 2개 그룹으로 나눠짐을 확인하였다. 또한 F. velutipes 4154 균주의 rDNA-cluster를 최초로 분석한 결과, 총 10,974 bp임을 밝혔다. SSU는 1,806 bp, ITS region은 553 bp의 염기배열이 결정되었다. ITS 1 부분은 245 bp이고 ITS 2는 308 bp였으며, LSU에 해당되는 염기서열은 3,402 bp, IGS 1은 1,400 bp, 5S는 83 bp, IGS 2는 3,571 bp임을 확인하였다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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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.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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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.