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Fig. 2 | BMC Plant Biology

Fig. 2

From: A pan-genomic approach to genome databases using maize as a model system

Fig. 2

MaizeGDB JBrowse pan-genome optimization. A Cross-referencing gene model annotations across the NAM Founders and B73v5. The panel on the left is the B73v5 JBrowse instance, demonstrating that a gene model annotation is truncated in the reference genome (1), but complete in the lifted over tracks (2) for Ms71 and B97, both of which are non-stiff-stalk temperate lines; Il14H, a sweet corn line, has all of the exons present but not the UTRs. HP301 (popcorn), CML247, and CML322 (tropical lines) are also truncated. (3) demonstrates that there is little RNA-seq expression at this locus in B73, and none in root tissue (red box). If a user clicks on the B97 gene model Zm00018ab410740 (4), a pop-up box opens; clicking on the link (5) it will take the user to the location of Zm00018ab410740 in the B97 browser (6). B97 Zm00018ab410740 RNA-seq (7) demonstrates robust expression in root tissue (red box), supporting the B97 gene model annotation, in contrast to the associated B73 locus, which has less RNA-seq support, particularly in root. The Ms71 locus shows similar root expression patterns but Il14H has no root expression (not shown). B Large-scale structural variants (SVs) (red = deletions, green = insertions) relative to B73v5 for two lines, B97, and tropical line CML103, and unmethylated regions (UMRs, blue) and ATAC-seq peaks (orange) for B73v5, B97, and CML103. All data are aligned against the reference B73v5 genome. (1) Deletions (red) relative to B73 that are only in B97 (the red spaces represent the regions in B73 missing in B97); these regions are not deleted in CML103, as indicated by the absence of the red spaces in that genome. (2) Deletion shared between B97 and CML103 relative to B73. (3) UMRs present at the same loci in B73, B97, and CML103. (4) UMRs present only in B73

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