Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family.

中文翻译：

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系统基因组同线性网络分析揭示了植物中生长素反应因子基因的祖先转座。

生长素反应因子（ARFs）长期以来一直是研究热点，代表了一类植物生长发育的关键调节因子。综合系统基因组同线性网络分析能够为 ARF 基因家族的进化提供新的见解。在这里，从植物基因组和转录组中收集的超过 3500 个 ARFs 涵盖了主要的链植物谱系，用于重建大范围的家族系统发育，其中描述了轮生植物中 ARF 的早期起源和多样化。基于家族系统发育，我们提出了被子植物ARFs的统一六组分类系统。系统基因组同线性网络分析揭示了六个 ARF 组中每个组中高度保守的基因组同线性以及连接不同组的互锁同线性关系。经常性重复事件，例如在种子植物、被子植物、核心真双子叶植物和禾本科植物中发生的那些促进了促进功能多样化的 ARF 基因的扩展。通过同线性网络分析揭示了重要植物家族（包括十字花科植物、豆科植物和草类）的祖先转座活动。祖先基因重复和转座具有深远的进化意义，这可能加速了旁系同源物的功能多样化过程。广泛的家族系统发育与最先进的系统基因组同线性网络分析相结合，不仅使我们能够推断 ARF 基因在不同植物谱系中的进化轨迹，而且有助于为该转录因子生成更强大的分类机制家庭。