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

Changwei Bi; Fei Shen; Fuchuan Han; Yanshu Qu; Jing Hou; Kewang Xu; Li-An Xu; Wenchuang He; Zhiqiang Wu; Tongming Yin

doi:10.1093/hr/uhae023

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

Hortic Res. 2024 Jan 23;11(3):uhae023. doi: 10.1093/hr/uhae023. eCollection 2024 Mar.

Authors

Changwei Bi^{1

2}, Fei Shen³, Fuchuan Han⁴, Yanshu Qu¹, Jing Hou¹, Kewang Xu¹, Li-An Xu¹, Wenchuang He⁵, Zhiqiang Wu⁵, Tongming Yin¹

Affiliations

¹ State 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.
² Department of artificial intelligence, College of Information Science and Technology, College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
³ Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
⁴ Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
⁵ Shenzhen 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.

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.