Recently, a team of researchers led by Wu Zhiqiang from the Institute of Genomics, along with Professor Jin Shuangxia from Huazhong Agricultural University and Henry Daniel from the University of Pennsylvania, were invited to publish a review titled "Plant organelles genes: many done, many more to do" in the internationally renowned botanical journal Trends in Plant Science. They systematically summarized the current sequencing abundance, mutation rate, and The research achievements in structural variation and other aspects have explored the important mechanisms that shape the evolutionary characteristics of organelles, and proposed important scientific questions worth exploring in the future. At the same time, the review explores the current mechanisms, applicability, limitations, and future challenges of genetic transformation and editing of organelles, providing a unique perspective on the improvement and development of plant organelle editing tools.

The unbalanced development of plant organelle sequencing

Chloroplasts and mitochondria are the only organelles in plants that possess an endosymbiotic origin genome, and are also the core sites for plant photosynthesis and respiration. Due to the difficulty in precise assembly of plant mitochondrial genomes, the current distribution of genome sequencing between organelles and taxa is extremely uneven. The large repetitive sequences and horizontal transfer fragments within the plant mitochondrial genome are important reasons for this difficulty. Therefore, it is necessary to conduct targeted research on the organelle genomes of key and rare evolutionary groups in the future, as well as focus on breaking through the development of plant mitochondrial genome specific assembly tools to address issues such as rare conformational capture.

Figure 1 | Number of plant organelle genomes generated by different sequencing methods from 2005 to March 2023

1. Evolutionary characteristics of plant organelle genome differentiation

The review provides a detailed comparison of the similarities and differences in gene content, mutation rate, structural variation, and horizontal transfer between two sets of organelle genomes in plants, and summarizes the potential mechanisms that affect different characteristics. The review calls for research on unknown functional ORFs in organelle genomes, as well as dynamic population changes and high-resolution conformational capture in organelle genomes. It emphasizes that exploring the RRR mechanisms of organelle genome inheritance, recombination, and repair is an important aspect of understanding mutations and structural variations. In addition, establishing a standardized evaluation system and identification method for intracellular horizontal transfer is an important step in understanding the evolution of the cellular genome.

Figure 2 | Mutations and structural variations in plant organelle genomes

2. Development and challenges of organelle gene editing technology

This review summarizes the achievements of chloroplast genetic transformation and its combined research with synthetic biology, and elucidates the limitations of complex changes in plant mitochondrial genome population dynamics on genetic transformation. In addition, this article focuses on comparing the technical characteristics, mechanisms of action, and limitations of emerging organelle gene editing systems such as TALENs, DdCBEs, and CyDENT. It proposes the future prospects of organelle gene editing work, including accurate acquisition of organelle genome whole tissue/developmental stage sequence and three-dimensional structural information, understanding of mitochondrial gene replication and translation processes, screening of strong selection markers, homogeneity sorting, and development of small molecular weight delivery systems.

Figure 3 | Plant organelle genome editing

3. Future challenges faced by organelle genome research

Finally, the review focuses on the population variation and 3D conformation of organelle genomes in different tissues/developmental stages between and within species, functional exploration of repetitive sequences and non coding regulatory elements in non coding regions, regulatory mechanisms of structural variation, and organelle gene editing, proposing a series of important scientific questions worth exploring in the future. It is worth mentioning that this paper is listed as the 2024 Feature Review, which is the type of article with the least quantity, longest length, and greatest influence among the types of articles published in Trends in Plant Science.

Figure 4 | Future work prospects of plant organelle genomes

Author Introduction

Researcher Wu Zhiqiang has been dedicated to the research of plant organelle genomes since 2006, utilizing omics big data to explore the variation and mutation mechanisms of organelle genomes, as well as the molecular mechanisms of cell nuclear cytoplasmic interactions, and exploring the transformation of organelle based photosynthesis systems to improve crop yield. In recent years, the research team has continuously published articles in journals such as PNAS (2015), Mol Biol Evol (2017), Heredity (2019), G3 (2020), JSE (20202022), and BMC Plant Biol (2023) analyzing the complexity and diversity of plant mitochondrial genome variations, which is of great significance for understanding and researching the complexity and diversity of life origin and evolution. The research group focused on the molecular mechanism of mutations and creatively confirmed through experimental evidence that the MSH1 gene has a dual function of regulating organelle genome recombination and mutation repair (PNAS, 2020), and further constructed a complete organelle genome variation map of the MSH1 Arabidopsis mutant (Plant J, 2022). In addition, the research group has developed for the first time a strategy in the field of organelle genomes to evaluate organelle structural variations using graphical plant mitochondrial genomes (Brief Bioinformation, 2023). The research group is currently recruiting postdoctoral fellows. Interested friends are welcome to contact Researcher Wu Zhiqiang（ wuzhiqiang@caas.cn ）. Jin Shuangxia is a professor at Huazhong Agricultural University and a recipient of the National Outstanding Youth Fund. From 2007 to 2012, he conducted postdoctoral research in Professor Henry Daniel's laboratory at the University of Pennsylvania in the United States, focusing on plant chloroplast (plastid) genetic engineering and synthetic biology. After returning to China, his team focused on cotton biotechnology and insect resistance genetic engineering research, created cotton genotypes with high somatic embryogenesis ability, developed multiple sets of gene editing tools, and continuously published high-level research papers in the field of plant biotechnology, forming a significant academic influence. He is the main research force in cotton biotechnology development internationally. Currently serving as Executive Editor of Plant Biotechnology Journal, Editor of Genome Biology, and Deputy Editor of Crop Journal. Wang Jie, a doctoral student at the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, and Kan Shenglong, a postdoctoral fellow (currently employed at Shandong University), as well as Liao Xuezhu, a doctoral student, are the co first authors of the paper. Wu Zhiqiang, a researcher at the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, Professor Jin Shuangxia from Huazhong Agricultural University, and Professor Henry Daniel from the University of Pennsylvania are the co corresponding authors. In addition, Zhou Jiawei, a doctoral student jointly trained by the Institute of Genomics and Central China Agricultural University, and Dr. Luke Tembrock from Colorado State University in the United States also participated in this work. This work has been supported by the National Natural Science Foundation of China, the National Science Fund for Distinguished Young Scholars, the Shenzhen Science and Technology Innovation Commission, the Young Talents of the Academy of Agricultural Sciences, the the Pearl River Talents of Guangdong Province and the Innovation Project of the Academy of Agricultural Sciences. Original link：https://www.cell.com/trends/plant-science/fulltext/S1360-1385(23)00412-0