Genomic distribution of simple sequence repeats in Brassica rapa.
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.
Hong
Chang Pyo
CP
Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 305-764, Korea.
Piao
Zhong Yun
ZY
Kang
Tae Wook
TW
Batley
Jacqueline
J
Yang
Tae-Jin
TJ
Hur
Yoon-Kang
YK
Bhak
Jong
J
Park
Beom-Seok
BS
Edwards
David
D
Lim
Yong Pyo
YP
D017360:Arabidopsis / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D018745:Genome, Plant; D018598:Minisatellite Repeats; D016366:Open Reading Frames