Fig. 2

Aligned genomic region in chr1 of Oryza nivara (top) and Oryza sativa Japonica group cv. Nipponbare (bottom) as displayed in the Ensembl Plants browser. Genes on the forward strand ( >) are above contigs, whilst those in the negative strand ( <) are underneath. As a result of the genomic alignment, genes of O. nivara overlap with gene models from O. sativa. This evidence can be used to identify collinear genes that take equivalent positions in different genomes, as illustrated with gene models ONIVA01G00130 and Os01g0100500, which overlap over 2.4 kb (yellow rectangle). The example shows that overlapping gene models might share only some exons. The table below shows the collinear gene models identified based on minimap2 and GSAlign alignments, together with the corresponding overlapped base pairs