Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes
文献类型： 外文期刊
作者： Wang, Jie 1 ; Kan, Shenglong 1 ; Kong, Jiali 1 ; Nie, Liyun 1 ; Fan, Weishu 5 ; Ren, Yonglin 3 ; Reeve, Wayne 2 ; Mower, Jeffrey P. 6 ; Wu, Zhiqiang 1 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,K, Shenzhen 518120, Peoples R China
2.Murdoch Univ, Sch Med Mol & Forens Sci, Perth, WA 6150, Australia
3.Murdoch Univ, Coll Environm & Life Sci, Perth, WA 6150, Australia
4.Shandong Univ, Marine Coll, Weihai 264209, Peoples R China
5.Chinese Acad Sci, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
6.Univ Nebraska, Ctr Plant Sci Innovat, Lincoln, NE 68588 USA
7.Univ Nebraska, Dept Agron & Hort, Lincoln, NE 68583 USA
关键词： plastid; substitution rate; inversion; repetitive DNA; inverted repeats; Plantago
期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.2； 五年影响因子：3.2 ）
ISSN： 1759-6653
年卷期： 2024 年 16 卷 8 期
页码：
收录情况： SCI
摘要： Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.
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