Fig. 3

Pan-genome and tandem array information on the gene model pages. Featured is information for the reference B73v5 gene model Zm00001eb360200. A The pan-gene tab (arrow) of Zm00001eb360200 and all syntenic orthologs for most maize lines hosted by MaizeGDB. Gene model information for syntenic orthologs (“gene model”) and the name of the genome (“assembly”) is provided. Collapsible sections for “Overview” (top) and “Orthologs in other species” (bottom) provide more information on how the pan-gene relationships were derived, and grass syntenic relationships, respectively. Many genomes have more than one representative; for instance, “Zm-CML52-REFERENCE-NAM-1.0” has two gene models in the set: Zm00019ab347600 and Zm00019ab347610; these are tandem duplications. B A partial screen capture of the gene model tab (arrow) with information about gene models that are tandem duplicates of the reference gene model Zm00001eb360200 (2) (Zm00001eb360210 and Zm00001eb360220) for a total of three gene copies, including the reference gene model. C A CoGe (https://genomevolution.org/) visualization alignment output of the tandem arrays for B73 and CML52 featured in A) and B). The green cartoons are gene models; the red boxes are blastn alignments of the coding regions between the two genomes. This image supports the MaizeGDB pipeline determination of tandem array copies in both B73 and CML52