Detailed description of the employed datasets for the genome-to-genome alignment, and the reads alignment with a reference sequence.

In these comparisons, the Illumina and PacBio data for Arabidopsis thaliana Ler-0 genome [68] are employed. Moreover, the human Illumina and PacBio reads are employed from the Ashkenazi child data set, which is available from the Genome in a Bottle project [69], NCBI SRA accession SRX847862. Furthermore, the reference genomes are the Arabidopsis thaliana Col-0 reference genome [62], human reference genome versionGRCH38.p7 [63], and the chimpanzee (pan troglodytes) genome [70], released in PanTro4, GenBank accession GCF0001515.6.