Genomic distribution of simple sequence repeats in Brassica rapa

Hong, Chang Pyo, Piao, Zhong Yun, Kang, Tae Wook, Batley, Jacqueline, Yang, Tae-Jin, Hur, Yoon-Kang, Bhak, Jong, Park, Beom-Seok, Edwards, David and Lim, Yong Pyo (2007) Genomic distribution of simple sequence repeats in Brassica rapa. Molecules and Cells, 23 3: 349-356.

Author Hong, Chang Pyo
Piao, Zhong Yun
Kang, Tae Wook
Batley, Jacqueline
Yang, Tae-Jin
Hur, Yoon-Kang
Bhak, Jong
Park, Beom-Seok
Edwards, David
Lim, Yong Pyo
Title Genomic distribution of simple sequence repeats in Brassica rapa
Formatted title
Genomic distribution of simple sequence repeats in Brassica rapa
Journal name Molecules and Cells   Check publisher's open access policy
ISSN 1016-8478
Publication date 2007-06-30
Sub-type Article (original research)
Volume 23
Issue 3
Start page 349
End page 356
Total pages 8
Place of publication Seoul, Republic of Korea
Publisher Korean Society for Molecular Biology
Language eng
Subject 060408 Genomics
060407 Genome Structure and Regulation
060102 Bioinformatics
Formatted abstract
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 pericentromeric 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.
Keyword Arabidopsis thaliana
Brassica rapa ssp. pekinensis
Genomic distribution
Simple Sequence Repeat (SSR)
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Institute for Molecular Bioscience - Publications
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Created: Thu, 15 Jan 2009, 12:11:22 EST by Judy Dingwall on behalf of Institute for Molecular Bioscience