Organism cells host genomes in distinct compartments: nucleus, chloroplast (for plants), and mitochondrion (both plant and animal). Chloroplast and mitochondria are the only organelles that possess genomes of endosymbiotic origin, and specifically, play important roles across the lifespan of organisms in respiration, photosynthesis, and numerous other metabolic pathways. Research on the two organellar genomes has answered many important questions regarding their evolution and function, however, an in-depth understanding is largely lacking of their variations within various evolutionary scales, structural dynamics, intracellular transfer, modification, and cytonuclear interactions, organellar genome editing, etc.

This special issue aims to seek innovative explorations into the assembly, evolutionary and functional variation, and applications of chloroplast and mitochondrial genomes. The topic includes an in-depth look at chloroplast/mitochondrial genome assembly methods like annotation and visualization, variation comparisons within and across different organism lineages, as well as an analysis focusing on intracellular gene transfers and evolutionary modifications and consequences. Moreover, we encourage the exploration of genome applications relating to organelle-based phylogenetics, population genomics, and pan-organelle genomes, as well as genome editing on organellar genomes. By integrating insights from both genomic dry data to experimental wet lab data on the organellar genome and combining comprehensive reviews of innovative research and computational methods, we aim to enhance our comprehensive understanding of organellar genomics, stimulate advancement in the arena of organellar genomics, and provide practical insights for the broader biological field.

Specific topics include, but are not limited to:

● Chloroplast phylogenetics of plants at/above the species level

● Mitochondrial genome assembly and variation comparison within and across diversified organism lineages

● Mechanism of intracellular gene transfer and post-transfer evolutionary dynamics

● Organellar genome editing for functional investigation 

Guest Editors

Dr. Zhiqiang Wu, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China

Dr. Wenpan Dong, Beijing Forestry University, China

Dr. Shenglong Kan, Shandong University, China

Deadline

The deadline for manuscript submissions is September 10, 2025, but we can accommodate extensions on a case-by-case basis. All papers will be published as open-access articles upon acceptance.

Submission Instructions

Please submit the full manuscript to Genomics Communications via our Online Submission System. Additionally, please choose a topic of this special issue when submitting and mention it in your cover letter. For further inquiries, please contact Guest Editors:

Zhiqiang Wu (wuzhiqiang@caas.cn)

Wenpan Dong (wpdong@bjfu.edu.cn)

Shenglong Kan (kanshenglong@sdu.edu.cn)