Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences.
Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences.
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水龙骨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
DOI：
10.1186/s12870-020-02800-x
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发表时间：
2021-01-07
影响因子：
5.3
通讯作者：
Wang T
中科院分区：
文献类型：
--
作者：
Liu S;Wang Z;Su Y;Wang T
背景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。水龙骨科是现存蕨类植物中物种最丰富且尚未开发的类群之一。人们普遍认为水龙骨科的质体在组织稳定性方面非常显着。因此，目前尚未对水龙骨科基因组结构变异进行研究。结果基于二代测序，确定了Neolepisorus Fortunei、Neolepisorus ovatus和Phymatosorus cuspidatus的完整质体序列。与已发表的质体组一起，对水龙骨科质体体的精细结构进行了比较分析。结果表明，水龙骨科的质体并不像之前假设的那样保守。水龙骨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 的质体表现出显着的特征，不仅包括超过数 kb 的大规模 IR 扩展，而且还具有独特的倒转。此外，还鉴定了水龙骨科质体中的基因内容、SSR、分散重复序列和突变热点区域。尽管分散的重复序列在水龙骨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。结论我们的结果表明，水龙骨科的质体是动态分子，而不是像之前认为的那样构成静态基因组。侧翼插入序列的分散重复序列有助于双链断裂诱导的修复机制，并且可能是水龙骨科质体结构进化的主要驱动力。
BackgroundComparative 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.ResultsThe complete plastome sequences ofNeolepisorus fortunei,Neolepisorus ovatus, andPhymatosorus cuspidatuswere 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 ofSelliguea yakushimensisexhibits 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.ConclusionsOur 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.
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DOI：
10.1007/bf02497656
发表时间：
1992-09-01
期刊：
BOTANICAL MAGAZINE-TOKYO
影响因子：
--
作者：
HASEBE, M;IWATSUKI, K
通讯作者：
IWATSUKI, K
影响因子：
4.1
作者：
Asano, T;Tsudzuki, T;Kadowaki, K
通讯作者：
Kadowaki, K
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
影响因子：
4.1
作者：
Kim, KJ;Lee, HL
通讯作者：
Lee, HL
影响因子：
3.7
作者：
Chen, Zhi-Duan;Yang, Tuo;Lu, An-Ming
通讯作者：
Lu, An-Ming