Journal of Plant Biotechnology

한국식물생명공학회 (The Korean Society of Plant Biotechnology)
권호 표지

Simple Sequence Repeat (SSR) and GC Distribution in the Arabidopsis thaliana Genome

  • Mortimer Jennifer C (Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Department of Plant Sciences, University of Cambridge) ;
  • Batley Jacqueline (Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University) ;
  • Love Christopher G (Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University) ;
  • Logan Erica (Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University) ;
  • Edwards David (Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University)
  • 발행 : 2005.03.01
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초록

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.

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