Mitochondrial Genome Study of American Ginseng Shows Changes in Gene Splicing

Greg Howard
18th August, 2024

Mitochondrial Genome Study of American Ginseng Shows Changes in Gene Splicing

Image Source: Natural Science News, 2024

Key Findings

  • Researchers successfully mapped the complete mitochondrial genome of American ginseng, revealing its genetic blueprint
  • They found a high number of repetitive DNA elements, adding to the genome's complexity
  • The study identified extensive genetic exchanges between the plant's chloroplast and mitochondrial genomes
Panax quinquefolius, commonly known as American ginseng, is a perennial plant renowned for its medicinal properties. A recent study by the Chinese Academy of Medical Sciences & Peking Union Medical College has made significant strides in understanding the mitochondrial genome (mitogenome) of this valuable plant[1]. This research could pave the way for enhanced medicinal applications and a deeper understanding of plant evolutionary biology. In this study, the researchers successfully assembled the complete mitogenome of P. quinquefolius using the PMAT assembler, a tool designed for efficient de novo assembly of plant mitogenomes from low-coverage HiFi sequencing data[2]. The total length of the mitogenome was determined to be 573,154 base pairs (bp). The team annotated 34 protein-coding genes (PCGs), 35 tRNA genes, and 6 rRNA genes within this mitogenome, providing a comprehensive genetic blueprint of the plant's energy metabolism organelles[3]. One of the intriguing findings of this study was the high frequency of repetitive elements within the P. quinquefolius mitogenome. The researchers identified 153 simple sequence repeats (SSRs), 24 tandem repeats, and 242 pairs of dispersed repeats. These elements contribute to the structural complexity and dynamic nature of the mitogenome. Similar complexity has been observed in other plant mitogenomes, such as those of the Cucurbitaceae family, where large genome sizes are attributed to the accumulation of chloroplast sequences and repeated sequences[4]. The study also highlighted the extensive sequence dialogue between the plastome (chloroplast genome) and the mitogenome of P. quinquefolius. The researchers found 24 homologous sequences, accounting for 41.05% of the plastome and 11.18% of the mitogenome. This frequent exchange of sequences between the two organelles underscores the intricate genetic interactions within plant cells and mirrors findings in other plants like Citrullus lanatus and Cucurbita pepo, where chloroplast sequences significantly contribute to the mitochondrial genome[4]. Another key aspect of the research was the identification of 583 C to U RNA editing sites across the 34 protein-coding genes. RNA editing is a post-transcriptional process that alters nucleotide sequences, thereby modifying the protein products. This process is crucial for the proper functioning of mitochondrial genes and has been observed in various plant species, including those within the Cucurbitaceae family[4]. The use of Deepred-mt, a predictive tool for RNA editing sites, allowed for high-confidence predictions, enhancing the accuracy of the study's findings. The researchers also explored the phylogenetic relationships of P. quinquefolius with other angiosperms based on mitochondrial PCGs. This analysis provides insights into the evolutionary history and genetic divergence of American ginseng relative to other flowering plants. Understanding these relationships is essential for tracing the evolutionary trajectories and adaptive mechanisms of different plant species[3]. A particularly novel discovery in this study was the observed shift from cis- to trans-splicing in two mitochondrial introns, cox2i373 and nad1i728. Splicing is a process that removes introns (non-coding regions) from RNA transcripts, and the shift from cis- (within the same molecule) to trans-splicing (between different molecules) indicates a complex evolutionary adaptation. The fragmentation and rearrangement of the cox2i373 intron, confirmed through PCR amplification experiments, further illustrate the dynamic nature of the mitogenome. This phenomenon of intron fragmentation and rearrangement has been noted in other plant studies, such as the fission of the mitogenome in Populus simonii[3]. In summary, the assembly and analysis of the P. quinquefolius mitogenome by the Chinese Academy of Medical Sciences & Peking Union Medical College provide crucial insights into the genetic and evolutionary dynamics of this medicinal plant. The findings, including the high frequency of repetitive elements, extensive sequence exchange between plastome and mitogenome, RNA editing sites, and the novel splicing mechanisms, contribute to our understanding of plant mitogenomes and their evolutionary adaptations. This research not only enhances our knowledge of P. quinquefolius but also sets the stage for future studies on the genetic mechanisms underlying plant medicinal properties.

GeneticsBiochemPlant Science

References

Main Study

1) Analysis of the complete mitochondrial genome of Panax quinquefolius reveals shifts from cis-splicing to trans-splicing of intron cox2i373.

Published 15th August, 2024

https://doi.org/10.1016/j.gene.2024.148869

Related Studies

2) PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data.

https://doi.org/10.1093/hr/uhae023

3) Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii.

https://doi.org/10.3389/fpls.2022.914635

4) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

https://doi.org/10.1093/molbev/msq029


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