水稻细胞器基因组中的简单序列重复：基因区域和基因间区域的频率与分布

Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions.

作者信息

Rajendrakumar Passoupathy, Biswal Akshaya Kumar, Balachandran Sena M, Srinivasarao Kommoju, Sundaram Raman M

机构信息

Biotechnology Laboratory, Crop Improvement Section, Directorate of Rice Research Rajendranagar, Hyderabad-500030, India.

出版信息

Bioinformatics. 2007 Jan 1;23(1):1-4. doi: 10.1093/bioinformatics/btl547. Epub 2006 Oct 31.

DOI:10.1093/bioinformatics/btl547

PMID:17077096

Abstract

MOTIVATION

Simple sequence repeats (SSRs) are abundant across genomes. However, the significance of SSRs in organellar genomes of rice has not been completely understood. The availability of organellar genome sequences allows us to understand the organization of SSRs in their genic and intergenic regions.

RESULTS

We have analyzed SSRs in mitochondrial and chloroplast genomes of rice. We identified 2528 SSRs in the mitochondrial genome and average 870 SSRs in the chloroplast genomes. About 8.7% of the mitochondrial and 27.5% of the chloroplast SSRs were observed in the genic region. Dinucleotides were the most abundant repeats in genic and intergenic regions of the mitochondrial genome while mononucleotides were predominant in the chloroplast genomes. The rps and nad gene clusters of mitochondria had the maximum repeats, while the rpo and ndh gene clusters of chloroplast had the maximum repeats. We identified SSRs in both organellar genomes and validated in different cultivars and species.

摘要

动机

简单序列重复（SSRs）在整个基因组中广泛存在。然而，水稻细胞器基因组中SSRs的重要性尚未完全被理解。细胞器基因组序列的可得性使我们能够了解SSRs在其基因区和基因间区域的组织情况。

结果

我们分析了水稻线粒体和叶绿体基因组中的SSRs。我们在线粒体基因组中鉴定出2528个SSRs，在叶绿体基因组中平均鉴定出870个SSRs。在线粒体的基因区观察到约8.7%的线粒体SSRs，在叶绿体的基因区观察到27.5%的叶绿体SSRs。二核苷酸是线粒体基因组基因区和基因间区域中最丰富的重复序列，而单核苷酸在叶绿体基因组中占主导地位。线粒体的rps和nad基因簇具有最多的重复序列，而叶绿体的rpo和ndh基因簇具有最多的重复序列。我们在两个细胞器基因组中都鉴定出了SSRs，并在不同品种和物种中进行了验证。