Additional file 1 of GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

Additional file 1: Table S1. Other Whole Genome Alignment stats for minimap2 and GSAlign algorithms. Table S2. Summary of BUSCO completeness analyses of individual genomes that are part of datasets in this paper. Table S3. Collinear genes found between Arabidopsis thaliana and A. lyrata within 23 blocks of the Ancestral Crucifer Karyotype based on Whole Genome Alignments produced with minimap2 and GSAlign. Table S4. Excerpt from BED-like pangene matrix produced during the analysis of dataset rice3. Table S5. Summary of Whole Genome Alignment (WGA) evidence for the gene models in CDS cluster Horvu_MOREX_1H01G011400 resulting from the analysis of dataset barley20. Figure S1. Overlap ratio of collinear gene models in rice, wheat and barley. Figure S2. Dot plots of collinear gene models called in rice, wheat and barley genomes. Figure S3. Venn diagrams of pangene clusters based on minimap2 and GSAlign Whole Genome Alignments of the rice3 dataset. Figure S4. Sequence identity among sequences in rice3 pangene clusters based on minimap2 (left) and GSAlign (right). Figure S5. Example of pangene cluster where the cDNA sequences have a long local alignment but the encoded CDS sequences cannot be aligned. Figure S6. Examples of rice pangene clusters not matched by Ensembl Compara orthogroups. Figure S7. Example of pangene cluster where the encoded protein sequences do not share protein domains. Figure S8. Flowchart of script check_evidence.pl , which uses as input a cluster in FASTA format and precomputed collinearity evidence in TSV format. Figure S9. Partial deletion of locus HvFT3/Ppd-H2 in barley cultivar Igri. Figure S10. Genomic context of pangene cluster HORVU.MOREX.r3.2HG0166090 (cluster members indicated with green arrows), which corresponds to barley locus HvCEN. Figure S11. Multiple alignment of protein sequences of pangene cluster HORVU.MOREX.r3.2HG0184740, which corresponds to barley locus Vrs1. Figure S12. Multiple alignment of protein sequences of pangene cluster HORVU.MOREX.r3.3HG0311160, which corresponds to barley locus HvOS2. Figure S13. Genomic context of pangene cluster gene:HORVU.MOREX.r3.7HG0752640, an example with tandem copies (cluster members indicated with green arrows), which encode acidic proteins