Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA

• 成果类型: Article
• 署名作者: Zwonitzer, Kendra D.; Tressel, Lydia G.; Wu, Zhiqiang; Kan, Shenglong; Broz, Amanda K.; Mower, Jeffrey P.; Ruhlman, Tracey A.; Jansen, Robert K.; Sloan, Daniel B.; Havird, Justin C.
• 署名单位: University of Texas System; University of Texas Austin; Chinese Academy of Agricultural Sciences; Agriculture Genomes Institute at Shenzhen, CAAS; Guangdong Laboratory for Lingnan Modern Agriculture; Shandong University; Colorado State University System; Colorado State University Fort Collins; University of Nebraska System; University of Nebraska Lincoln
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-14704
• DOI: 10.1073/pnas.2317240121
• 发表日期: 2024-03-05
• 关键词: substitution rates; homologous recombination; phylogenetic analysis; inverted repeat; relative rates; mutation-rate; repair; chloroplast; heteroplasmy; ORGANIZATION

摘要

Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000 - fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing -300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift- barrier hypothesis.