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

文献类型： 外文期刊

作者： Bi, Changwei 1 ; Shen, Fei 3 ; Han, Fuchuan 4 ; Qu, Yanshu 1 ; Hou, Jing 1 ; Xu, Kewang 1 ; Xu, Li-an 1 ; He, Wenchuang 5 ; Wu, Zhiqiang 5 ; Yin, Tongming 1 ;

作者机构： 1.Nanjing Forestry Univ, Coinnovat Ctr Sustainable Forestry Southern China, Key Lab Tree Genet & Biotechnol Educ Dept China, State Key Lab Tree Genet & Breeding,Key Lab Tree G, Nanjing 210037, Peoples R China

2.Nanjing Forestry Univ, Coll Informat Sci & Technol, Dept Artificial Intelligence, Nanjing 210037, Peoples R China

3.Beijing Acad Agr & Forestry Sci, Inst Biotechnol, Beijing 100097, Peoples R China

4.Chinese Acad Forestry, Res Inst Subtrop Forestry, Hangzhou 311400, Peoples R China

5.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,K, Shenzhen 518000, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 3 期

页码：

收录情况： SCI

摘要： 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 1x 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.

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