Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
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DOI：
10.1105/tpc.010479
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发表时间：
2002-07-01
期刊：
影响因子：
11.6
通讯作者：
Tanksley, SD
中科院分区：
文献类型：
--
作者：
Fulton, TM;Van der Hoeven, R;Tanksley, SD
我们已经筛选了一个大的番茄EST数据库对拟南芥基因组序列，并在这里报告的一组1025个基因（称为保守的直系同源物集，或COS标记），这是单拷贝或低拷贝的两个基因组（由计算屏幕和DNA凝胶印迹杂交确定），并已保持相对稳定的序列，因为早期辐射的双子叶植物的鉴定。这些基因被注释，并且大部分可以被分配到与基本代谢过程相关的推定功能类别，例如能量产生过程以及细胞构建块的生物合成和降解。我们进一步证明，通过计算屏幕（例如，对蒺藜苜蓿数据库）和在不同植物物种的基因组DNA上的直接杂交，这些COS标记在其它植物科的基因组中也是保守的。最后，我们表明，该基因集可用于高度分歧的基因组，如番茄和拟南芥基因组之间的比较映射研究。这组COS标记，通过计算和实验确定，可能进一步研究比较基因组和植物遗传学和阐明在整个植物进化过程中保守的基因的性质。
We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel blot hybridization) and that have remained relatively stable in sequence since the early radiation of dicotyledonous plants. These genes were annotated, and a large portion could be assigned to putative functional categories associated with basic metabolic processes, such as energy-generating processes and the biosynthesis and degradation of cellular building blocks. We further demonstrate, through computational screens (e.g., against a Medicago truncatula database) and direct hybridization on genomic DNA of diverse plant species, that these COS markers also are conserved in the genomes of other plant families. Finally, we show that this gene set can be used for comparative mapping studies between highly divergent genomes such as those of tomato and Arabidopsis. This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.