芸苔属植物中长末端重复序列反转录转座子爆发的独立和多轮热点区域

Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species

Abstract  抽象的

Long terminal repeat retrotransposons (LTR-RTs) are a predominant group of plant transposable elements (TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes of the agronomically important oil and vegetable crops of the genus Brassica. Herein, full-length LTR-RTs in the genomes of Brassica and other closely related species were systematically analyzed. The full-length LTR-RT content varied greatly (from 0.43% to 23.4%) between different species, with Gypsy-like LTR-RTs constituting a primary group across these genomes. More importantly, many annotated LTR-RTs (from 10.03% to 33.25% of all detected LTR-RTs) were found to be enriched in localized hotspot regions. Furthermore, all of the analyzed species showed evidence of having experienced at least one round of a LTR-RT burst, with Raphanus sativus experiencing three or more. Moreover, these relatively ancient LTR-RT amplifications exhibited a clear expansion at specific time points. To gain a further understanding of this timing, Brassica rapa, B. oleracea, and R. sativus were examined for the presence of syntenic regions, but none were present. These findings indicate that these LTR-RT burst events were not inherited from a common ancestor, but instead were species-specific bursts that occurred after the divergence of Brassica species. This study further exemplifies the complexities of TE amplifications during the evolution of plant genomes and suggests that these LTR-RT bursts play an important role in genome expansion and divergence in Brassica species.

**摘要**：长末端重复序列反转录转座子（LTR-RTs）是植物转座元件（TEs）的一个主要类群，也是植物基因组的重要组成部分。在具有重要农业价值的芸苔属油料和蔬菜作物的基因组中，已注释了大量LTR-RTs。在此，我们系统分析了芸苔属及其他密切相关物种基因组中的全长LTR-RTs。不同物种的全长LTR-RT含量差异很大（从0.43%到23.4%），其中Gypsy型LTR-RTs是这些基因组中的主要类群。更重要的是，许多注释的LTR-RTs（占所有检测到的LTR-RTs的10.03%到33.25%）富集于局部热点区域。此外，所有分析的物种都显示出至少经历过一轮LTR-RT爆发的证据，其中萝卜（Raphanus sativus）经历了三次或更多次。此外，这些相对古老的LTR-RT扩增在特定时间点表现出明显的扩张。为了进一步了解这一时间点，我们对甘蓝型油菜（Brassica rapa）、甘蓝（B. oleracea）和萝卜进行了同源区域的检测，但未发现任何同源区域。这些发现表明，这些LTR-RT爆发事件并非来自共同祖先的遗传，而是芸苔属物种分化后发生的物种特异性爆发。本研究进一步揭示了植物基因组进化过程中转座元件扩增的复杂性，并表明这些LTR-RT爆发在芸苔属物种的基因组扩张和分化中发挥了重要作用。

1. Introduction

Repeat sequences are a major constituent of plant genomes and play an important role in plant genome evolution. Of the repeat sequences, transposable elements (TEs) are a significant component. Within the genomes of Arabidopsis and maize, TEs comprise over 14% and 80% of the genome sequences, respectively (Arabidopsis Genome, 2000,