The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing Gypsy LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.

除多倍体外，转座因子（transposable element, TE）是推动植物基因组体积扩增的主要因素。因此，解析向日葵（Helianthus annuus L.）中转座因子的多样性与进化动态具有重要意义——该物种基因组体积庞大（约3.5 Gb），且该属内已被充分记录存在特定转座子扩增事件，这一研究对理解这一新兴模式物种的进化历史至关重要。本研究通过随机测序读段与组装的细菌人工染色体（bacterial artificial chromosome, BAC）克隆，对约25%的向日葵基因组进行分析，结果显示其基因组中超过81%的序列为转座因子，其中77%为长末端重复序列逆转录转座子（long terminal repeat retrotransposon, LTR反转录转座子）。进一步分析发现，在携带基因的BAC克隆中，LTR反转录转座子组分显著富集含染色质结构域的Gypsy型LTR反转录转座子（又称chromoviruses），且绝大多数完整的这类染色质病毒均包含串联式染色质结构域重复。本研究证实，同源重组清除LTR反转录转座子DNA的效率存在偏好性，这为解析向日葵基因组中转座因子组成的相关机制提供了新见解。同时，本研究发现观测到的绝大多数LTR反转录转座子插入事件均发生在该物种起源之后，进一步证明具有偏好性的LTR反转录转座子活性在塑造向日葵基因组的染色质与DNA景观中发挥了核心作用。尽管本研究关于LTR反转录转座子年龄与结构的结论可能受所分析BAC克隆选择的影响，但对随机测序读段的全局分析表明，本文揭示的进化模式适用于整个向日葵基因组。