GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

Table 4 Summary of pangene clusters obtained for datasets ACK2 and rice3 and the corresponding orthogroups in Ensembl Plants. Core clusters contain genes from all analyzed genomes; in rice, shell clusters contain genes from two species. BUSCO completeness percentages for core sets are shown in parentheses. Clusters with multiple copies have several genes from the same species. gDNA segments are shell clusters that bring together a gene model and a matching genomic segment from the underlying WGA. Column ‘match Compara’ shows the number of pangene clusters that contain the same genes as the corresponding Compara orthogroups. The last column shows the number of pangene clusters that contain sequences that share an InterPro domain (the number in square brackets is for core clusters only)

	Dataset	Core clusters [%BUSCO]	Multiple copies	Shell clusters	gDNA segments	Match Compara	Share InterPro domains
Compara orthogroups	ACK2	20,192 [90.6]	161				[18,259]
minimap2 clusters	ACK2	20,647 [94.1]	731			18,245	[18,792]
GSAlign clusters	ACK2	16,476 [74.9]	454			14,181	[14,817]
Compara orthogroups	rice3	13,020 [65.6]	219	6386			16,766 [11,571]
minimap2 clusters	rice3	22,880 [85.2]	3360	7825	6521	18,281	23,062 [19,239]
GSAlign clusters	rice3	20,399 [84.6]	2885	9730	6103	17,103	22,834 [17,135]

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