The rice mitochondrial genomes and their variations
The rice mitochondrial genomes and their variations
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DOI：
10.1104/pp.105.070060
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发表时间：
2006-02-01
期刊：
影响因子：
7.4
通讯作者：
Yu, J
中科院分区：
文献类型：
--
作者：
Tian, XJ;Zheng, J;Yu, J
基于高度冗余和高质量的序列，我们组装了两个品种93-11（籼稻品种）和PA64S（母系粳稻的类籼品种）的水稻（Oryza sativa）线粒体基因组，这两个品种分别是优良超级杂交水稻良优培九（LYP-9）的父本品系和母本品系。继之前对水稻叶绿体基因组的分析之后，我们将线粒体序列变异分为两个基本类别：品种内变异和亚种间变异。品种内多态性是单个品种线粒体基因组内的变异。亚种间多态性是亚种之间主要基因型之间的变异。在这项研究中，我们鉴定了 96 个单核苷酸多态性 (SNP)、25 个插入缺失和 3 个片段序列变异作为亚种间多态性。通过实验证实了籼稻品种特有的特征序列片段，并在两个野生稻样品中发现了该序列片段，但在粳稻品种中不存在。线粒体基因组的亚种间多态性率（SNP）为 0.02%，插入/缺失为 0.006%，分别比叶绿体亚种间多态性低近 2.5 倍和 3 倍，比水稻核基因组相应亚种间多态性低 21 倍和 38 倍。所分析的线粒体基因组（例如 93-11 和 PA64S）的种内多态性率，SNP 分别为 1.26% 和 1.38%，插入缺失分别为 1.13% 和 1.09%。根据两个线粒体基因组之间的 SNP 总数，我们估计籼稻和粳稻线粒体基因组的分歧发生在大约 45,000 至 250,000 年前。
Based on highly redundant and high-quality sequences, we assembled rice ( Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S ( an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite superhybrid rice Liang-You-Pei-Jiu (LYP-9), respectively. Following up with a previous analysis on rice chloroplast genomes, we divided mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms are variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms are variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms ( SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties was confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes is 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts and 21 and 38 times lower than corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs and 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago.