*4.4. Repeat Estimation in Organelle Genomes*

Repeat content was estimated in four mitogenomes and 13 plastomes (Table 2). Tandem repeats were identified using Tandem Repeats Finder version 4.09 [66] with default options. Other repeats (larger than 30 bp) were analyzed by BLASTN [63] searches using each genome as both subject and query with a word size of 7 and an e-value of 1e−<sup>6</sup> as described in Guo et al. [67]. All BLAST hits were retained. Sequence coordinate information for BLAST hits was transferred to each genome as an annotation in Geneious and overlapping regions between hits were excluded from the estimations for repetitive DNA content. The distribution of dispersed repeat sequences across the genomes was visualized by Circoletto [68].
