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
Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 305-764, Korea.
Mol Cells. 2007 Jun 30;23(3):349-56.
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.
简单序列重复（SSRs）是在所有真核生物中发现的短串联重复序列。为了研究白菜型油菜北京变种基因组中SSRs的分布情况，我们对代表17.7 Mb基因组序列的不同基因组区域中的SSRs进行了调查。SSRs在非编码区（86.6%）比在编码区（13.4%）更为丰富。不同基因组区域中SSRs密度的比较表明，预测基因的5'侧翼区域内的SSRs密度最大。不同重复基序的比例在基因组区域之间有所不同，三核苷酸SSRs在预测的编码区更为普遍，这反映了这些区域的密码子结构。SSRs也优先与基因丰富的区域相关联，着丝粒周围的异染色质SSRs大多与反转录转座子相关。这些结果表明，基因组中SSRs的分布是非随机的。白菜型油菜与近缘物种拟南芥之间SSRs丰度的比较表明白菜型油菜中SSRs更为丰富，这可能是由于推测的基因组三倍化所致。我们的结果提供了一个关于白菜型油菜中SSRs基因组分布和进化的全面视图，以便与拟南芥和水稻的测序基因组进行比较。
