毛竹全长LTR逆转座子的鉴定和进化分析

Identification and Evolutionary Study of Full-length LTR-retrotransposons in Moso Bamboo Genome

转座子和逆转座子的大量插入,是高等植物基因组进化的重要动力。作为植物基因组研究热点的禾本科植物之一,毛竹基因组大小约为2 Gb,60%为重复序列,长末端重复序列型逆转座子（LTR逆转座子）则占全部重复序列的一半以上,然而目前对毛竹基因组中LTR逆转座子及进化情况知之甚少。本研究利用已发表的毛竹基因组序列,首次通过大数据筛查预测获得9 436个平均长度10.3 kb的全长LTR逆转座子。通过分析,我们估算出毛竹LTR逆转座子插入基因组的时间主要分布于200~500万年前,晚于毛竹基因组四倍化的时间。研究还发现了29个位于全长LTR逆转座子内部、有转录组序列支持的蛋白编码基因,这些毛竹基因均不符合所在基因组区段的毛竹-水稻基因共线性关系,且位于LTR逆转座子内部的基因与存在于染色体其他位置的同源基因在表达模式上有着较大差异。本研究首次尝试从LTR逆转座子的角度探索毛竹基因的进化历程,也为今后的植物基因组研究提供了重要的基础数据。

Accumulation of transposable elements, including transposons and retrotransposons, is the primary contributor to genome evolution in higher plants. As a grass species, moso bamboo has a 2 Gb genome in size and 60% is covered by repetitive sequences. Of these repetitive sequences, over 50% is long terminal repeat retrotran- sposons （LTR-retrotransposons）, however, we know little about the role of the LTR-retrotransposons in evolution of moso bamboo genome. In this study, a total of 9,436 full-length LTR-retrotransposons with an average length of 10.3 kb were predicted by genome-wide data processing in moso bamboo. The estimated insertion ages of the LTR-retrotransposons are mainly at 2 to 5 million years ago, which is later than tetraploidization of the moso bamboo genome. Twenty-nine protein-coding genes were revealed to be located inside the full-length LTR-retro- transposons. Each of them is supported by RNA-seq data and does not show gene collinearity in the corresponding bamboo-rice-synteny region. Different gene expression patterns are observed between the gene inside the LTR-retrotransposon and its homolog outside it. The present study of moso bamboo LTR-retrotransposons provides a potential mechanism of genes evolution, The data set of the identified full-length LTR-retrotransposons will be the fundamental data source for genome research oflalants.