• Genomics & Informatics
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• 제20권3호
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• pp.35.1-35.9
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• 2022

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

• 한국버섯학회지
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• 제19권4호
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• pp.341-346
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• 2021

국내의 주요 산느타리 품종인 호산47(일핵, 산타리 배우자), GB19(일핵, 산타리 배우자), 호산, 여름느타리1호, 삼복, 강산, 약산, 자산, 향산, 여름느타리2호의 유전체를 Hiseq을 이용하여 해독하였고 이 서열 정보에서 SSR을 분리하여 특성구명을 하였다. 일핵균사인 호산 47, GB19의 유전체의 크기는 각각 37.3와 37.2 Mbp이고, 이핵균사인 나머지 산느타리 품종의 유전체 크기는 47.1~61.1 Mbp인 것으로 밝혀졌다. 품종별 총 SSR의 수는 HS47이 711개로 가장 적고, 강산이(GS)이 1.5배 많은 1,106개로 최다를 기록하였다. SSR의 repeat motif 중에서 hexanucleotide와 octanucleotide가 가장 많은 빈도로 관찰되었고, 가장 많이 관찰되는 반복서열은 CGA/TCG, A/T, CTC/GAG이었다. SSR의 길이는 모든 품종에서 변이가 많아 유용성이 높은 20~30 nt가 가장 높은 비중인 70%를 차지하였다.

• Journal of Plant Biotechnology
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• 제4권2호
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• pp.45-52
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• 2002

A lot of SSRs (simple sequence repeats) in peach and pear from enriched genomic libraries and in peach from a cDNA library were developed. These SSRs were applied to other related species, giving phenograms of 52 Prunes and 60 pear accessions. Apple SSRs could also be successfully used in Pyrus spp. Thirteen morphological traits were characterized on the basis of the linkage map obtained from an $F_2$ population of peach. This map was compiled with those morphological markers and 83 DNA markers, including SSR markers used as anchor loci, to compare different peach maps. Molecular markers tightly linked to new root-knot nematode resistance genes were also found. A linkage map including disease related genes, pear scab resistance and black spot susceptibility, in the Japanese pear Kinchaku were constructed using 118 RAPD markers. Another linkage map, of the European pear Bartlett, was also constructed with 226 markers, including 49 SSRs from pear, apple, peach and cherry. Maps of other Japanese pear cultivars, i.e., Kousui and Housui, were also constructed. These maps were the first results of pear species.

• Molecules and Cells
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• 제23권3호
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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.

• Molecules and Cells
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• 제27권2호
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• pp.237-241
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• 2009

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

• 한국식물생명공학회:학술대회논문집
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• 한국식물생명공학회 2002년도 추계학술대회
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• pp.101-109
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• 2002

A lot of SSRs (simple sequence repeats) in peach and pear from enriched genomic libraries and in peach from a cDNA library were developed. These SSRs were applied to other related species, giving phenograms of 52 Prunus and 60 pear accessions. Apple SSRs could also be successfully used in Pyrus spp. Thirteen morphological traits were characterized on the basis of the linkage map obtained from an $F_2$ population of peach. This map was compiled with those morphological markers and 83 DNA markers, including SSR markers used as anchor loci, to compare different peach maps. Molecular markers tightly linked to new root-knot nematode resistance genes were also found. A linkage map including disease-related genes, pear scab resistance and black spot susceptibility, in the Japanese pear Kinchaku were constructed using 118 RAPD markers. Another linkage map, of the European pear Bartlett, was also constructed with 226 markers, including 49 SSRs from pear, apple, peach and chewy. Maps of other Japanese pear cultivars, i.e., Kousui and Housui, were also constructed. These maps were the first results of pear species.

• 한국식물생명공학회:학술대회논문집
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• 한국식물생명공학회 2002년도 춘계학술대회
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• pp.101-109
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• 2002

A lot of SSRs (simple sequence repeats) in peach and pear from enriched genomic libraries and in peach from a cDHA library were developed. These SSRs were applied to other related species, giving phenograms of 52 Prunus and 60 pear accessions. Apple SSRs could also be successfully used in Pyrus spp. Thirteen morphological traits were characterized on the basis of the linkage map obtained from an Fa population of peach. This map was compiled with those morphological markers and 83 DHA markers, including SSR markers used as anchor loci, to compare different peach maps. Molecular markers tightly linked to new root-knot nematode resistance genes were also found. A linkage map including disease-related genes, pear scab resistance and black spot susceptibility, in the Japanese pear Kinchaku were constructed using 118 RAPD markers. Another linkage map, of the European pear Bartlett, was also constructed with 226 markers, including 49 SSRs from pear, apple, peach and cherry. Maps of other Japanese pear cultivars, i.e., Kousui and Housui, were also constructed. These maps were the first results of pear species.

• 식물분류학회지
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• 제52권3호
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• pp.156-172
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• 2022

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

• 한국버섯학회지
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• 제14권4호
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• pp.174-178
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• 2016

SSR은 병렬적으로 반복되는 작은 DNA서열을 말하며, 다양한 마커 기반 연구에 활용되고 있다. 국내의 주요 느타리품종인 '흑타리'와 '미소'의 유전체를 Pacbio를 이용하여 해독하였고 이 서열 정보에서 생물정보학을 이용하여 SSR을 분리하여 특성구명을 하였다. '흑타리'와 '미소' 유래 단핵균사의 유전체의 크기는 각각 40.8 Mbp와 40.3 Mbp로 밝혀졌고, 이는 사철느타리의 단핵균사 PC9과 PC15보다 컸으나, 큰느타리보다는 작았다. 총 949개와 968개의 SSR이 '흑타리'와 '미소'의 유전체 분석을 통하여 각각 검출되었다. 5개의 느타리류 유전체의 SSR 분포와 특징을 비교분석한 결과 흑타리와 미소의 SSR 갯수가 가장 많았으며, 이들의 반복서열의 분포는 다른 느타리류와 비슷한 경향을 보였다. 3-mers, 6-mers와 8-mers가 가장 발견빈도가 높은 패턴이었다.

• Journal of Plant Biotechnology
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• 제7권1호
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• pp.17-25
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• 2005

We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the genome and a strong association within and around transcribed sequences, while G/C density is associated specifically with the coding portions of transcribed sequences. SSR motif repeat number shows a high degree of variation for each SSR type and a high degree of motif sequence bias reflecting local genome sequence composition. PCR primers suitable for the amplification of identified SSRs have been designed where possible, and are available for further studies.