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RESEARCH PRODUCT

A workflow to assemble plant mitochondrial genomes using long-reads: case study in Pisum sativum and Phaseolus vulgaris

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Plant mitochondrial genomes are generally not used to study evolution within and between species. They are larger than animal mitochondrial genomes and evolve by accumulating rearrangements rather than mutations [1]. These characteristics make it difficult to obtain complete assemblies using short-reads like in mammals. To address this problem, we developed and tested a plant-based assembly workflow using Nanopore and Pacbio long-reads from Pisum sativum and Phaseolus vulgaris, respectively. Nanopore long-reads from Pisum sativum whole genome sequencing and Pacbio long-reads from Phaseolus vulgaris whole genome sequencing were mapped on all mitochondrial genomes available for legumes at NCBI using minimap2. Captured reads were assembled using canu 1.8 and corrected by racon for Nanopore reads and pilon for both using available Illumina reads. Circlator was used to circularize the sequences obtained. To assess and compare gene orders, the annotation of each mitochondrial genome was done using GeSeq. A phylogeny based on mitochondrial gene order was built and showed consistency with legumes’ reported phylogeny. Illumina short reads from wild pea accessions were also mapped to the mitochondria of Pisum sativum to identify putative gene order differences. These resources pave the way for further use of legume and other plant mitochondrial data to answer evolution-related key questions.