Assemble plant mitochondrial genome with short reads - insights into the mitochondrial genome evolution of Fagales

The nonconservation and uncertain structure of plant mitochondrial genomes make the assembly a big challenge. So far, in angiosperms, the known mitochondrial genomes are much less than plastid genomes. For many species, the mitochondrial genome becomes the last genome in the cell that undeciphered, e.g. in Fagales, more than 20 nuclear genomes and 150 plastid genomes are known but no more than two mitochondrial genomes were formally published. To close the gap and improve the quality of plant mitochondrial genome assemblies, we developed a reliable workflow and assembled 23 complete and high-quality mitochondrial genomes of Fagales by using short Illumina sequencing reads.