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 distrib...
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.
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.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
제안 방법
The program SPUTNIK (Abajian 1994, http://abajian.net/ sputnik/) was applied, in combination with custom perl scripts, to identify SSRs within a series of overlapping windows of 100 Kb with a 1 Kb step, across the five Ara bidopsis chromosomes and within each of the additional datasets. The criteria for SSR discovery was a minimum repeat length of 5 repeat units for dinucleotide repeats, 4 repeat units for trinucleotide repeats, 3 repeat units for tetranucleotide repeats and 2 repeat units for pentanu cleotide repeats.
org). These data included five complete chromosome seqences, and multi fasta files representing exons, introns, coding sequence, intergenic regions, 3' UTRs (UnTranslated Regions), 5' UTRs and 1000 bp and 3000 bp regions flanking expressed genes. The original gene flan king sequence datasets represented mixtures of UTR and non-UTR containing sequences.
대상 데이터
Arabidopsis thaliana sequence datasets were obtained from TAIR (The Arabidopsis Genome Initiative 2000; http://www.arabidopsis.org). These data included five complete chromosome seqences, and multi fasta files representing exons, introns, coding sequence, intergenic regions, 3' UTRs (UnTranslated Regions), 5' UTRs and 1000 bp and 3000 bp regions flanking expressed genes.
성능/효과
It was found that the transcribed sequences exhibited a higher overall frequency of SSRs than non-transcribed se quences for all the sections of the transcribed regions ex cept for the exons. Although exons showed high densities of trinucleotide repeats, all other repeats occured at very low frequencies.
Examination of the proportion of each motif sequence allowed the identification of SSR sequence bias between genomic regions. The proportions of dinucleotide repeat motif sequences were shown to be similar across all genomic regions, with the exception of the 5* UTR and exon subsets which contained 89.52% [AG]n dinucleotide SSRs, and 85.85% [AT]n dinucleotide SSRs respectively (supplementary data).
This study identified a total of 44,316 SSRs over 116.89 Mb of the complete seqence of the five A. thaliana chromosomes, giving an overall density of 379.29 SSRs per Mb with SSRs making up a total of 0.5% of the A. thaliana genome.
참고문헌 (35)
Abajian C (1994) SPUTNIK
Arhondakis S, Auletta F, Torelli G, D'Onofrio G (2004) Base composition and expression level of human genes. Gene 325: 165-169
Awadalla P, Ritland K (1997) Microsatellite variation and evolution in the Mimulus guttatus species complex with contracting mating systems. Mol Biol Evol 14: 1023-1034
Brandes A, Thompson H, Dean C, Heslop-Harrison JS (1997) Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L. Chromosome Res 5: 238-246
Dieringer D, Schlotterer C (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 1: 2242-2251
Gupta M, Chyi Y-S, Romero-Severson J, Owen JL (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89: 998-1006
Holland JB, Hellend SJ, Sharopova N, Rhyne DC (2001) Polymorphism of PCR based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat. Genome 44: 1065-1076
Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48: 501-510
Khashnobish A, Hamann A, Osiewacz HD (1999) Modulation of gene expression by (CA)(n) microsatellites in the filamentous ascomycete Podospora anserina. Applied Microbiol Biotech 52: 191-195
Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11: 2453-2465
Lowenhaupt KY, Rich A, Pardue ML (1989) Nonrandom distribution of long mono-nucleotide and dinucleotide repeats in Drosophila chromosomes - correlations with dosage compensation, heterochromatin and recombination. Mol Cell Biol 9: 1173-1182
Nanda I, Zischler H, Epplen C, Gutlenbach M, Schmid M (1991) Chromosomal organisation of simple repeated DNA Sequences used for DNA fingerprinting. Electrophoresis 12: 193-203
Pardue ML, Lowenhaupt K, Rich A, Nordheim A (1987) (DCDA)N.(DG-DT)N sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function. EMBO J 6: 1781-1789
Ramsay L, Macaulay M, Cardle L, Morgante M, degli Ivanissevich S, Maestri E, Powell W, Waugh R (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J 17: 415-425
Ross CL, Dyer KA, Erez T, Miller SJ, Jaenike J, Markow TA (2003) Rapid divergence of microsatellite abundance among species of Drosophila. Mol Biol Evol 20: 1143-1157
Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4: R13
Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silica analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7: 537-546
Weber JL (1990) Informativeness of human $(DC-DA)_n. (DG-DT)_n$ polymorph isms. Genomics 7: 524-530
※ AI-Helper는 부적절한 답변을 할 수 있습니다.