Extended Data Fig. 2: Sugar accumulation candidate gene alignments.
From: The complex polyploid genome architecture of sugarcane
A) Alignment of syntenic orthologs for SUT4 (Sobic.008G193300). B) Alignment of syntenic orthologs for SIP2 (Sobic.002G075800). C) Alignment of syntenic orthologs for PME (Sobic.005G082100). Top section for each panel shows the full length of the alignment, while the bottom section displays a zoomed in region (outlined in a pink dotted outline) to show specific differences among species and alleles. Prog- progenitor assignment of R570 alleles. Each ortholog position was intersected with progenitor assignments to assign origin to each peptide. %PID- Percent pairwise identity (number of matches/alignment length * 100) for each syntenic ortholog relative to the S. bicolor (BTx623). Copy number (CN)- PacBio HiFi read depths (representing collapsed identical haplotypes) ranges were intersected with gene position to provide an indication of additional collapsed alleles (eg. copy number = 2; one represented allele + one identical collapsed allele). Fold score (FS)- syntenic orthologs (except for monoploid annotated peptides) were folded using ESMfold and scored for quality. Score provided is the percent of high-quality amino acids present in the peptide sequence.
