MINI REVIEW article
Front. Plant Sci.
Sec. Plant Bioinformatics
This article is part of the Research TopicEvolutionary Dynamics, Functional Variation and Application of Plant Organellar Genome, volume IIView all articles
From genome assembly to functional interpretation: an epistemological shift in understanding plant mitochondrial architecture
Provisionally accepted
Tianchao Wang1Hao He1Jinwei Sun1Jie Man1Jiawei Li1Zheng Kuang1Yifei Liu2*
Zhenyu Huang3*
Yongxin Zhao1*- 1Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- 2College of Horticulture and Forestry, Tarim University, Aral, China
- 3Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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The plant mitochondrial genome exhibits high complexity and structural diversity, which pose major challenges to its accurate assembly and in-depth interpretation. In recent years, the rapid advancement of sequencing technologies has driven the development of multiple assembly tools tailored for plant mitochondrial genomes. This review systematically summarizes recent progress in plant mitochondrial genome assembly, focusing on several representative computational tools, including GetOrganelle, GSAT, HIMT, PMAT, TIPPo, and PMAT2, and discusses their algorithmic principles, major advantages, and potential limitations. Furthermore, we highlight the methodological transition of mitochondrial genomics from traditional static sequence reconstruction to dynamic structural modeling. Finally, we outline future perspectives in data integration, standardization, and community benchmarking, which will collectively contribute to establishing a unified analytical framework for interpreting the complexity of plant mitochondrial genomes.
Keywords: plant mitochondrial genome, genome assembly, long-read assembly, Graph-based assembly, Algorithm Evaluation
Received: 13 Oct 2025; Accepted: 17 Nov 2025.
Copyright: © 2025 Wang, He, Sun, Man, Li, Kuang, Liu, Huang and Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Yifei Liu, yf71@foxmail.com
Zhenyu Huang, huangzhenyu@caas.cn
Yongxin Zhao, yongxinzhaozyx@163.com
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