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CC BY V4.0, Open Access
Journal article
Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes
Genome biology and evolution, Vol.16(8)
2024
PMID: 39190481
Abstract
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.
Details
- Title
- Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes
- Authors/Creators
- Jie Wang - Agricultural Genomics Institute at ShenzhenShenglong Kan - Agricultural Genomics Institute at ShenzhenJiali Kong - Henan UniversityLiyun Nie - Agricultural Genomics Institute at ShenzhenWeishu Fan - Institute of Genetics and Developmental BiologyYonglin Ren - Murdoch UniversityWayne Reeve - Murdoch University, Centre for Sustainable Farming SystemsJeffrey P Mower - University of Nebraska–LincolnZhiqiang Wu - Agricultural Genomics Institute at Shenzhen
- Publication Details
- Genome biology and evolution, Vol.16(8)
- Publisher
- Oxford University Press on behalf of Society for Molecular Biology and Evolution.
- Grant note
- ; 32170238 / ; 110243160001007 / ; RCYX20200714114538196 / ;
- Identifiers
- 991005699966407891
- Copyright
- © The Author(s) 2024.
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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