Fig. 5

The proposed model for the evolutionary HSA2 fusion event based on the assembled SD-rich subtelomeric sequences in Great Apes chromosomes, absent in the reference genomes. The fusion site is flanked proximally and distally, respectively, by the ~190 kb and ~68 kb SDs homologous to human chromosomes 9p24.3 and 22q13.33 (98.9% and 97.8-99.1% sequence identity). The ~190 kb fragment harbouring FOXD4L1 (red solid rectangle) (Fig. 4), and likely originating from an ancestral locus syntenic to chromosome 9q21.11 in human, was previously shown to be duplicatively transposed to chromosome PTR2Apter after gorilla had branched off the common chimp-human ancestor lineage (Additional file 1: Table S3-S5) [20, 36, 46, 47]. Both copies flank the evolutionarily pericentromeric inversion in the human and chimp genomes that arose after the gorilla divergence [36, 45, 47]. We have proposed that a portion of the PTR9pter copy was also copied onto chromosome PTR22qter and later PTR2Bter before the gorilla-chimp divergence [36, 45, 48, 49]. Importantly, our assemblies revealed substantially long homology (~190kb) between the lost fragments (within the yellow band) of the ancestral chromosomes 2Apter (Pre HSA2A) and 2Bpter (Pre HSA2B) that might have served as a substrate of misalignment during meiosis. The fusion occurred within TAR1 satellite and degenerate telomeric repeats present in both Pre HSA2Apter and Pre HSA2Bpter. Submicroscopic subtelomeric rearrangements in human are relatively common cause of genomic imbalances in patients with developments delay/intellectual disability [50]. Analyses of these sequences showed that two copies of the following six protein coding genes FOXD4L1, JMJD7-PLA2G4B, MAPKBP1, SPTBN5, CBWD2, and MALRD1, one pseudogene PGM5P4, and three lncRNAs LINC01881, LINC01961, and PGM5P4-AS1 might have been lost during the fusion event (Fig. 4, Additional file 1: Fig. S9)