Interdisciplinary Program in Agriculture Biotechnology, Seoul National University, Seoul 151-921, Korea.
BMC Genomics. 2011 Jan 29;12:85. doi: 10.1186/1471-2164-12-85.
Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.
For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.
Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.
在茄科植物中，辣椒的基因组是番茄的三倍。尽管这两个物种的基因库和基因顺序都很好地保存了下来，但基因组大小差异的原因尚不清楚。为了确定辣椒常染色质区域扩张的原因，我们将辣椒基因组与番茄基因组进行了比较。
为了进行序列水平的分析，我们从富含常染色质的 1245 个辣椒 BAC 克隆中生成了 35.6Mb 的辣椒基因组序列。对两个物种的同源基因丰富区域的比较分析表明，转座子仅在辣椒序列中插入，保持了基因的顺序和含量。发现的最常见的转座子类型是 LTR 反转录转座子。LTR 反转录转座子的系统发育比较表明，两组 Ty3/Gypsy 样元件（Tat 和 Athila）在辣椒基因组中过度积累。对辣椒 Tat 元件的 FISH 分析表明，它们在异染色质和常染色质区域中呈随机分布，而番茄 Tat 元件则表现出异染色质优先积累的特点。
与番茄相比，辣椒的常染色质大小增加了一倍，这是由一组特定的 Ty3/Gypsy 样元件的差异积累造成的。我们的研究结果可以为茄科植物家族的基因组进化机制提供新的认识。
