PanGenomes - MaizeOmics (A comprehensive multidimensional omics resource for maize (<em>Zea mays</em>))

Pan-gene Summary

We first evaluated the performance of aligner BLASTP in identifying syntelogs. The alignment results were filtered to retain only the best hits, and DAGchainer was employed to detect syntenic genomic regions and syntelogs. BLASTP was executed with an e-value cutoff of 1e-10, and syntelogs were identified using the same pipeline. These syntelogs derived from BLASTP were subsequently used in the downstream pan-genome construction. Tandem duplicates were treated as a single gene in the final pan-genome using DupGen_finder. Pairwise syntelog information was then incrementally merged using Mo17T2T as the initial framework via pansg (https://pydigger.com/pypi/pansg).

Pan-gene tree (Evolutionary tree based on the number of collinear genes)

Summary of annotations and assemblies included in the analysis

Assembly name	# of gene models	Max length	Average length	% placed in pan-genes

Pan-gene List

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All synterlog clusters are shown as below, click the syntelog ID to show detail.