Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation.
Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation.
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DOI：
10.1186/1471-2164-8-283
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发表时间：
2007-08-20
期刊：
影响因子：
4.4
通讯作者：
King I
中科院分区：
文献类型：
--
作者：
Armstead I;Huang L;King J;Ougham H;Thomas H;King I
已经开发了各种方法来探索植物物种之间的基因组间关系。在这里，我们提出了一个序列相似性分析的基础上比较转录组装和甲基化过滤数据库从五种植物和物理锚定水稻编码序列。通过MegaBLAST确定的TIGR假分子和注释vs4.0中的水稻编码序列与来自多年生黑麦草（黑麦草）、玉米（玉蜀黍）、大麦（大麦）、大豆（大豆）和拟南芥（塔勒水芹）的综合转录组装和甲基化过滤数据库之间的序列比对频率进行了比较。每个水稻假分子被分成10个片段，每个片段含有10%的功能注释的表达基因。这表明水稻基因组中的相对片段位置与所有查询的单子叶和双子叶植物数据库的比对数量之间存在相关性。使用沿着每个假分子的100个功能注释的表达基因的颜色编码移动窗口来生成“热图”。这些揭示了与测试的植物数据库显著比对的相对浓度的一致的假分子内和假分子间变化。对热图中“热点”和“冷点”水稻基因的注释和推导出的推定表达模式的分析表明了可能的功能差异。与水稻基因组的祖先重复有关的类似比较表明，重复通常与“热点”有关。水稻基因组中表达基因的物理位置与其他植物转录组中相似序列的保守程度相关。这种相对保守性与不同大小的基因家族和片段重复位点的分布有关，可能具有功能和进化意义。
Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.
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影响因子：
3.3
作者：
Parkin, IAP;Gulden, SM;Lydiate, DJ
通讯作者：
Lydiate, DJ
DOI：
10.1073/pnas.0502365102
发表时间：
2005-09-13
影响因子：
11.1
作者：
Bowers, JE;Arias, MA;Paterson, AH
通讯作者：
Paterson, AH
TIGR玉米数据库。
影响因子：
14.9
作者：
Chan, Agnes P.;Pertea, Geo;Cheung, Foo;Lee, Dan;Zheng, Li;Whitelaw, Cathy;Pontaroli, Ana C.;SanMiguel, Phillip;Yuan, Yinan;Bennetzen, Jeffrey;Barbazuk, William Brad;Quackenbush, John;Rabinowicz, Pablo D.
通讯作者：
Rabinowicz, Pablo D.
影响因子：
3.3
作者：
Federico, Maria L.;Iniguez-Luy, Federico L.;Kaeppler, Heidi F.
通讯作者：
Kaeppler, Heidi F.
DOI：
10.1073/pnas.0307901101
发表时间：
2004-06-29
影响因子：
11.1
作者：
Paterson, AH;Bowers, JE;Chapman, BA
通讯作者：
Chapman, BA