Fig. 4

Long-read sequencing reveals underlying structural variation among chromosomes. Segments of four germline contigs (1–4) rearrange to produce nine high-confidence isoforms (A-I) of one somatic chromosome, Contig14329.0. The four germline contigs most likely represent two paralogous loci; contig 2 terminates in repetitive sequences at both ends. These match repetitive sequence at the 3′ end of contig 3 and the 5′ end of contig 4. Dotted lines indicate that a contig extends beyond the region shown. Dark gray blocks on the germline contigs represent somatic sequence that is 100% identical between the two paralogs, while colored sequence represents regions that differ between the two germline loci. Colored segments in the somatic isoforms indicate the corresponding germline segments of origin; two boxes stacked vertically indicate ambiguity when the germline paralogs are identical. While most isoforms contain only sequence from one locus or the other, isoforms “A,” “B,” “D,” and “I” have variants that incorporate sequence from both loci, suggesting that alternative fragmentation and assembly can recombine segments from multiple loci, in addition to variable retention of segments within a single locus