Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
复制标题
DOI：
10.1101/gr.3869505
复制
发表时间：
2005-09-01
期刊：
影响因子：
7
通讯作者：
Jackson, S
中科院分区：
文献类型：
--
作者：
Nelson, W;Soderlund, C;Jackson, S
水稻(Oryza sativa L.)3号染色体在进化上在种植的谷物中是保守的，并与玉米和高粱有很大的同源性，后者在5000多万年前从水稻中分离出来。为了开始完全理解这条染色体，我们对野生稻亚种的36.1 Mb(类似于97%)进行了测序、完成和注释。日本报刊。该染色体的注释特征包括5915个基因，其中913个与转座元件相关。一个假定的功能可以被分配给3064个基因，另有757个基因被注释为表达，剩下的2094个基因编码假设的蛋白质。与拟南芥蛋白质组的相似性搜索显示，67%的3号染色体蛋白质可能是同源的。进一步搜索非冗余氨基酸数据库、Pfam结构域数据库、植物表达序列标签以及高粱和玉米的基因组组合，发现3号染色体上只有853个与非转座元件相关的蛋白质与其他已知序列缺乏相似性。有趣的是，其中426个在水稻基因组中有一个平行序列。野生祖先种Oryza nivara与日本3号染色体的比较物理图谱显示，这两个物种之间具有高度的序列同一性和同步性，类似于1万年前的分化。虽然没有检测到较大的重排，但推测的日本野生稻3号染色体的大小比粳稻的小21%。利用整合的玉米物理图谱和小麦遗传图谱，水稻和其他谷物之间的同步性惊人地高，进一步支持使用水稻，特别是3号染色体，作为谷物之间比较研究的模型。
Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (similar to 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged similar to 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further Supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.