Jiang Ning, Gao Dongying, Xiao Han, van der Knaap Esther
Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
Plant J. 2009 Oct;60(1):181-93. doi: 10.1111/j.1365-313X.2009.03946.x. Epub 2009 Jun 6.
DNA sequences provide useful insights into genome structure and organization as well as evolution of species. We report on a detailed analysis of the locus surrounding the tomato (Solanum lycopersicum) fruit-shape gene SUN to determine the driving force and genome environment that foster the appearance of novel phenotypes. The gene density at the sun locus is similar to that described in other euchromatic portions of the tomato genome despite the relatively high number of transposable elements. Genes at the sun locus include protein-coding as well as RNA genes, are small in size, and belong to families that were duplicated at the locus an estimated 5-74 million years ago. In general, the DNA transposons at the sun locus are older than the RNA transposons, and their insertion pre-dates the speciation of S. lycopersicum and S. pimpinellifolium. Gene redundancy and large intergenic regions may explain the tolerance of the sun locus to frequent rearrangements and transpositions. The most recent transposition event at the sun locus involved Rider, a recently discovered high-copy retrotransposon. Rider probably arose early during the speciation of tomato. The element inserts into or near to genes and may still be active, which are unusual features for a high-copy element. Rider full-length and read-through transcripts past the typical transcription termination stop are detected, and the latter are required for mobilizing nearby sequences. Rider activity has resulted in an altered phenotype in three known cases, and may therefore have played an important role in tomato evolution and domestication.
DNA序列为洞察基因组结构与组织以及物种进化提供了有用的信息。我们报告了对番茄（Solanum lycopersicum）果实形状基因SUN周围位点的详细分析，以确定促成新表型出现的驱动力和基因组环境。尽管转座元件数量相对较多，但SUN位点的基因密度与番茄基因组其他常染色质区域所描述的相似。SUN位点的基因包括蛋白质编码基因和RNA基因，它们体积较小，属于约在500万至7400万年前在该位点发生复制的基因家族。一般来说，SUN位点的DNA转座子比RNA转座子更古老，其插入早于番茄和醋栗番茄的物种形成。基因冗余和大的基因间区域可能解释了SUN位点对频繁重排和转座的耐受性。SUN位点最近的转座事件涉及Rider，这是一种最近发现的高拷贝逆转座子。Rider可能在番茄物种形成早期出现。该元件插入基因内部或附近，可能仍然活跃，这对于高拷贝元件来说是不寻常的特征。检测到Rider的全长转录本以及越过典型转录终止位点的通读转录本，后者对于动员附近序列是必需的。在三个已知案例中，Rider的活性导致了表型改变，因此可能在番茄进化和驯化过程中发挥了重要作用。
