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Article|26 Jan 2024|OPEN
PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data
Changwei Bi1,2 ,† , Fei Shen3 ,† , Fuchuan Han4 ,† , Yanshu Qu1 , Jing Hou1 , Kewang Xu1 , Li-an Xu1 , Wenchuang He5 and Zhiqiang Wu5 , , Tongming Yin,1 ,
1State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
2Department of artificial intelligence, College of Information Science and Technology, College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
3Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
4Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
5Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
*Corresponding author. E-mail: wuzhiqiang@caas.cn,tmyin@njfu.edu.cn
†Changwei Bi and Fei Shen,Fuchuan Han contributed equally to the study.

Horticulture Research 11,
Article number: uhae023 (2024)
doi: https://doi.org/10.1093/hr/uhae023
Views: 39

Received: 23 Aug 2023
Accepted: 14 Jan 2024
Published online: 26 Jan 2024

Abstract

Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity. Here, we present an efficient assembly toolkit (PMAT) for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. PMAT has been applied to the de novo assembly of 13 broadly representative plant mitogenomes, outperforming existing organelle genome assemblers in terms of assembly accuracy and completeness. By evaluating the assembly of plant mitogenomes from different sequencing data, it was confirmed that PMAT only requires 1× HiFi sequencing data to obtain a complete plant mitogenome. The source code for PMAT is available at https://github.com/bichangwei/PMAT. The developed PMAT toolkit will indeed accelerate the understanding of evolutionary variation and breeding application of plant mitogenomes.