• Molecules and Cells
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• v.20 no.3
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• pp.348-353
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• 2005

Using in silico approaches and RACE we cloned a full length trinucleotide (CAG) repeat-containing cDNA (cag-3). The cDNA is 2478 bp long and the deduced polypeptide consists of 140 amino acids of which 73 are glutamines. The genomic sequence spans approximately 79 kb on mouse chromosome 7 and the gene is composed of four exons. Standard and real-time PCR analyses of several mouse tissues showed that the gene is exclusively expressed in the brain and is not detected in embryonic stages. Within the brain, it is expressed throughout the forebrain region with predominant expression in the hypothalamus and olfactory bulb and very low levels in the mid- and hindbrain.

• Genomics & Informatics
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• v.7 no.4
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• pp.181-186
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• 2009

Myotonic dystrophy type 1 (DM1), which is a dominantly inherited neurodegenerative disorder, results from a CTG trinucleotide repeat expansion in the 3'-untranslated region (3'-UTR) of the myotonic dystrophy protein kinase (DMPK) gene. Retention of mutant DMPK (mDMPK) transcripts in the nuclei of affected cells has been known to be the main cause of pathogenesis of the disease. Thus, reducing the RNA toxicity through elimination of the mutant RNA has been suggested as one therapeutic strategy against DM1. In this study, we suggested RNA replacement with a trans -splicing ribozyme as an alternate genetic therapeutic approach for amelioration of DM1. To this end, we identified the regions of mDMPK 3'-UTR RNA that were accessible to ribozymes by using an RNA mapping strategy based on a trans-splicing ribozyme library. We found that particularly accessible sites were present not only upstream but also downstream of the expanded repeat sequence. Repair or replacement of the mDMPK transcript with the specific ribozyme will be useful for DM1 treatment through reduction of toxic mutant transcripts and simultaneously restore wild-type DMPK or release nucleus-entrapped mDMPK transcripts to the cytoplasm.

• Molecules and Cells
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• v.23 no.3
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• pp.349-356
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• 2007

Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.38-38
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• 2018

The genus Carduus (Asteraceae), containing ca. 90 species, is mainly distributed in Eurasia and Africa. Carduus species are one of the most hazardous invasive species, which causes serious environmental threats and biodiversity damages in North America. Thus, the member of Carduus are targeted for classical biological control in this region. Here, we provide the complete cp genome of Carduus crispus using next-generation sequencing technology. The size of cp genomes of C. crispus is 152,342 bp. It shows a typical quadripartite structure, consisting of the large single copy (LSC; 83,254 bp), small single copy (SSC; 18,706 bp), separated by a pair of inverted repeats (IRs; 25,191 bp). It contains 115 unique genes of which 21 genes duplicated in the IR regions. The cpSSR regions of Carduus species were searched through the complete chloroplast genome sequence using a tandem repeat search tool in Geneious with the parameters set to ${\geq}7$ mononucleotide repeats, ${\geq}4$ di- and trinucleotide repeats, and ${\geq}3$ tetra-, penta-, and hexanucleotide repeats. A total of 22 repeat motifs were identified, which may be useful for molecular identification of Korean Carduus species (C. cripus), and providing a guideline for its conservation.

• Horticultural Science & Technology
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• v.31 no.6
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• pp.772-781
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• 2013

The objective of this study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (EST) of lettuce (Lactuca sativa) and identify 9 germplasms from 3 wild species of lettuce and 61 commercial cultivars using the developed EST-SSR markers. A total of 81,330 lettuce ESTs from NCBI databases were used to search for SSR and 4,229 SSR loci were identified. The highest proportion (59.12%, 2500) was represented by trinucleotide, followed by dinucleotide (29.70%, 1256) and hexanucleotide (6.62%, 280) among SSR repeat motifs. Totally 474 EST-SSR primers were developed from EST and a random set of 267 primers was used to assess the genetic diversity among 9 germplasms and 61 cultivars. Out of 267 primers, 47 EST-SSR markers showed polymorphism between 7 cultivars. Twenty-six EST-SSR markers among 47 EST-SSR markers showed high polymorphism, reproducibility, and band clearance. The relationship between 26 markers genotypes and 70 accessions was analyzed. Totally 127 polymorphic amplified fragments were obtained by 26 EST-SSR markers and two to nine SSR alleles were detected for each locus with an average of 4.88 alleles per locus. Average polymorphism information content was 0.542, ranging from 0.269 to 0.768. Genetic distance of clusters ranged from 0.05 to 0.94 between 70 accessions and dendrogram at a similarity of 0.34 gave 7 main clusters. Analysis of genetic diversity revealed by these 26 EST-SSR markers showed that the 9 germplasms and 61 commercial cultivars were discriminated by marker genotypes. These newly developed EST-SSR markers will be useful for cultivar identification and distinctness, uniformity and stability test of lettuce.

• Journal of Marine Life Science
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• v.6 no.1
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• pp.38-46
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• 2021

The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.