Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
Genes (Basel). 2019 Jan 15;10(1):50. doi: 10.3390/genes10010050.
The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato () consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.
模式生物中基因功能的知识是分析非模式物种（包括具有经济重要性的物种）中基因功能的起点。通常，基因功能的分配是基于序列相似性。在植物中，由于基因景观非常复杂，这种方法存在一些局限性。通常不可能仅基于序列将一个植物物种的基因集直接与另一个物种的基因集相匹配。因此，有必要使用其他信息来识别功能相似的基因。表达模式具有作为此类信息来源的巨大潜力。进行转录组比较分析的一个重要前提是存在由可比样本组成的高分辨率表达图谱。在这里，我们展示了一个番茄（）的转录组图谱，该图谱由 30 个不同器官和发育阶段的样本组成。选择这些样本的方式允许与 转录组图谱并排比较。新获得的数据集成在 TraVA 数据库中，并在线提供，同时还提供了用于分析它们的工具。在本文中，我们展示了比较转录组图谱以推断旁系同源基因表达变化的潜力。
