PanViewer is a new GrainGenes tool currently under development that facilitates the exploration of pan-genes across wheat, barley, and oat genomes. PanViewer has been developed to provide researchers with an intuitive, user-friendly platform for visualizing and comparing pan-gene sequence diversity, gene presence–absence variation, and homoeologous relationships across major cereal crops. A total of 16 wheat genomes, 77 barley genomes, and 33 oat genomes have been processed using Pandagma, a method developed for pan-gene annotation that takes into account homoeologous chromosomes. This approach offers more accurate clustering of genes across complex polyploid genomes, particularly in wheat and oat, where distinguishing homoeologs is essential for meaningful comparative analysis. Additionally, the OrthoFinder-based pan-gene annotations obtained from the PanBARLEX and PanOat projects were added to PanViewer and are available to view independently of the Pandagma pan-gene annotations. PanViewer also enables users to quickly download pan-gene gene lists, coding sequences (CDS), and predicted protein sequences for downstream analyses. Integrated tools allow researchers to overlay gene expression data, explore synteny and collinearity relationships across genomes, construct protein alignments and phylogenetic trees, and assess sequence conservation relative to selected reference genes. Together, these features make PanViewer a powerful and flexible resource for comparative genomics and functional analysis in small grains research.

https://graingenes.org/panviewer/