Detection of Numts and data generation
Plant Numt insertions were identified using BLASTN local alignment tools in the BLAST program package (ver. 2.2.26), with mitochondrial genomic DNA as a query sequence and each genome dataset as a BLAST database. The execution options included an e-value cutoff set to 0.01, filtering switched off (-dust no), a mismatch penalty of –2, and a word size of 9. The neighboring Numt hits within 10 kb were, if necessary, merged into a single event of Numt insertions. All of these analytical processes were carried out with in-house Python codes.