Fig. 4
From: High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Resolution of the At4g30720 duplication using the KBS-Mac-74 ONTmin genome. Col-0 only has one copy of At4g30720 on the distal end (15 Mb) of chromosome 4 (Chr4). KBS-Mac-74 (ONTmin) assembly has two copies of At4g30720; one at the beginning of contig 31 that corresponds to the SG3 QTL location, and one at the distal end of contig 31 that overlaps with the SG3 interacting (SG3i) region in the middle of chromosome 4. At the SG3i locus, the Col-0 gene At4g08995 (889 bp), which is annotated as a transposable element (RT; putative reverse transcriptase), is replaced in the KBS-Mac-74 ONTmin assembly with a 39-kb expansion that includes a duplicated copy of At4g30720. Fragments of the transposable element (different gray arrows) are scattered across the KBS-Mac-74 region consistent with several rounds of transposition resulting in this complex rearranged region
