Comparative chloroplast genomics could shed light on the major evolutionary events that established plastomic diversity among closely related species. The Polypodiaceae family is one of the most species-rich and underexplored groups of extant ferns. It is generally recognized that the plastomes of Polypodiaceae are highly notable in terms of their organizational stability. Hence, no research has yet been conducted on genomic structural variation in the Polypodiaceae. The complete plastome sequences of Neolepisorus fortunei, Neolepisorus ovatus, and Phymatosorus cuspidatus were determined based on next-generation sequencing. Together with published plastomes, a comparative analysis of the fine structure of Polypodiaceae plastomes was carried out. The results indicated that the plastomes of Polypodiaceae are not as conservative as previously assumed. The size of the plastomes varies greatly in the Polypodiaceae, and the large insertion fragments present in the genome could be the main factor affecting the genome length. The plastome of Selliguea yakushimensis exhibits prominent features including not only a large-scale IR expansion exceeding several kb but also a unique inversion. Furthermore, gene contents, SSRs, dispersed repeats, and mutational hotspot regions were identified in the plastomes of the Polypodiaceae. Although dispersed repeats are not abundant in the plastomes of Polypodiaceae, we found that the large insertions that occur in different species are mobile and are always adjacent to repeated hotspot regions. Our results reveal that the plastomes of Polypodiaceae are dynamic molecules, rather than constituting static genomes as previously thought. The dispersed repeats flanking insertion sequences contribute to the repair mechanism induced by double-strand breaks and are probably a major driver of structural evolution in the plastomes of Polypodiaceae.

中文翻译：

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息肉科叶绿体的比较基因组分析揭示了精细的结构特征和动态插入序列

比较叶绿体基因组学可以揭示在密切相关的物种之间建立质体多样性的主要进化事件。Polypodiaceae 科是现存蕨类植物中物种最丰富且未被充分开发的类群之一。人们普遍认为，Polypodiaceae 的塑性体在其组织稳定性方面非常显着。因此，尚未对息肉科的基因组结构变异进行研究。Neolepisorus Fortunei、Neolepisorus ovatus 和 Phymatosorus cuspidatus 的完整塑性体序列是基于二代测序确定的。与已发表的塑性体一起，对息肉科塑性体的精细结构进行了比较分析。结果表明，Polypodiaceae 的塑性体并不像先前假设的那样保守。息肉科的质体大小差异很大，基因组中存在的大插入片段可能是影响基因组长度的主要因素。Selliguea yakushimensis 的塑性体表现出突出的特征，不仅包括超过几 kb 的大规模 IR 扩展，而且还具有独特的反转。此外，在 Polypodiaceae 的质体中鉴定了基因含量、SSR、分散的重复序列和突变热点区域。虽然分散的重复在息肉科的质体中并不丰富，但我们发现不同物种中发生的大插入是可移动的，并且总是与重复的热点区域相邻。我们的研究结果表明，Polypodiaceae 的质体是动态分子，而不是像以前认为的那样构成静态基因组。