Progress in Research on Heterogeneity of Plant Mitochondrial Genome Replacement Rate

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The evolution of genetic diversity is one of the core issues of evolutionary genomes. Angiosperm mitochondrial genomes are diverse in size, structure, genes, and intron numbers. This feature makes the mitochondrial gene composition an ideal system for studying the complexity of genomes. It is generally believed that the evolutionary speed of the plant mitochondrial genome is lower than that of the chloroplast genome and nuclear genome, and the evolution rate between genes within the same genome is more consistent. However, early studies on mitochondrial genomes of some taxa such as Ajuga reptans found that the rate of synonymous substitution between genes can differ by more than two orders of magnitude, and the evolutionary path and cause are unclear.


Recently, Zhu Andan and Li Deba, the researchers of the Plant Diversity and Genomics team at the Kunming Institute of Botany, Chinese Academy of Sciences, based on the National Major Scientific Project Wildlife Germplasm Resource Library of Southwest China, the mitochondrial genomes of 9 species and 19 species in all four main branches of Ajugoideae under Lamiaceae, were analyzed in-depth and systematically to analyze the occurrence time and related mechanisms of the substitution rate heterogeneity in the mitochondrial genome. The study found that the synonymous substitution rate (dS) is generally higher than the non-synonymous substitution rate (dN) in the mitochondrial genome of Ajugoideae subfamily, and the acceleration time of different genes in the same genome is different: some genes accelerate in the core group (core Ajugoideae) (such as rps12, etc.), some of them appear in the group of the genus Lysimachia and its sister genera (such as atp6, etc.), and some only appear in the group of the genus Ajuga (such as ccmC, etc.), but the substitution rate in several modes reached the maximum in the genus Lysimachia.



Further research found that most of the genes with the fastest change in substitution rate are located in gene clusters, and most of these gene clusters are newly formed in the Hyoscyamus and its sisters’ genus. The formation of new gene clusters has to go through the fragmentation of ancient gene clusters, and the fusion of new gene clusters, so it is speculated that mutations are easily introduced during this process, resulting in an increased rate of gene mutations. Due to the GC preference for genome recombination and gene conversion, the GC3 level of the third codon of the gene encoding the mitochondrial protein has been found to show that there is a significant increase in almost all rapid evolution genes in the genus Lysimachia, and the increase in GC3 content is significantly related to dS. The increase in substitution rate may also be affected by factors such as transcription-mediated repair or post-transcriptional modification, which may be manifested in the loss of RNA editing sites.


In this study, combined with transcriptome data analysis, it was found that genes that evolved rapidly lost all ancestral RNA editing sites, while genes that evolved at moderate and low speeds lost only a few ancestral RNA editing sites. This study analyzes the diversity of plant mitochondrial genome substitution rate, and speculates on the mechanism of heterogeneity of synonymous substitution rate within the mitochondrial genome, which provides theoretical support for the in-depth study of the evolution of plant mitochondrial genome complexity.

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