Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny

A 105-kilobase bacterial artificial chromosome (BAC) clone from the ovate-containing region of tomato chromosome 2 was sequenced and annotated. The tomato BAC sequence was then compared, gene by gene, with the sequenced portions of the Arabidopsis thaliana genome. Rather than matching a single portion of the Arabidopsis genome, the tomato clone shows conservation of gene content and order with four different segments of Arabidopsis chromosomes 2–5. The gene order and content of these individual Arabidopsis segments indicate that they derived from a common ancestral segment through two or more rounds of large-scale genome duplication events—possibly polyploidy. One of these duplication events is ancient and may predate the divergence of the Arabidopsis and tomato lineages. The other is more recent and is estimated to have occurred after the divergence of tomato and Arabidopsis ≈112 million years ago. Together, these data suggest that, on the scale of BAC-sized segments of DNA, chromosomal rearrangements (e.g., inversions and translocations) have been only a minor factor in the divergence of genome organization among plants. Rather, the dominating factors have been repeated rounds of large-scale genome duplication followed by selective gene loss. We hypothesize that these processes have led to the network of synteny revealed between tomato and Arabidopsis and predict that such networks of synteny will be common when making comparisons among higher plant taxa (e.g., families).

本研究对番茄2号染色体含卵形果基因（ovate）区域的105千碱基对细菌人工染色体（bacterial artificial chromosome，BAC）克隆进行了测序与注释。随后将该番茄BAC序列逐基因与拟南芥（Arabidopsis thaliana）基因组的已测序区段进行比对。结果显示，该番茄克隆并未匹配拟南芥基因组的单个区域，而是与拟南芥2至5号染色体的四个不同区段在基因含量与基因顺序上均存在保守性。这些单个拟南芥区段的基因顺序与含量表明，它们源自一个共同的祖先区段，经历了两轮或多轮大规模基因组复制事件——可能为多倍化。其中一次复制事件较为古老，其发生时间或早于拟南芥与番茄谱系的分化节点；另一次则相对较新，据推测发生在番茄与拟南芥约1.12亿年前分化之后。综上，这些数据表明，在BAC级别的DNA区段尺度上，染色体重排（如倒位与易位）仅为植物间基因组组织分化的次要影响因素，而主导因素为多轮大规模基因组复制事件，随后伴随选择性基因丢失。我们据此提出假说：上述过程造就了番茄与拟南芥之间已发现的共线性（synteny）网络，并预测在高等植物类群（如科一级）间开展比较研究时，这类共线性网络将普遍存在。