Fig. 3

Evaluation of the assembly result. a Heatmap of the query coverage of alignment of each contig of the indica dispensable genome to different Oryza genomes. Each row represents a contig and each column denotes a sequenced genome. Only the contigs that could be aligned to the non-reference genome with improved match length (≥100 bp longer) compared with the alignment to the Nipponbare reference genome are shown. O. brachyantha and O. glaberrima are both Oryza species, Nipponbare is the rice reference genome, 93-11 is a typical rice variety belonging to the indica subspecies, and W1943 is a representative accession of Oryza rufipogon. b PCR validation of 11 DNA fragments from the randomly selected contigs of the indica dispensable genome. For each DNA fragment, two PCR results (two adjacent lanes) are shown. The lanes marked with contig names are PCR results using DNA of the selected rice accessions while the unmarked lanes are PCR results using DNA of Nipponbare (see Additional file 5 for more details). Lanes marked with “Actin” are the PCR results with actin using DNA of the Nipponbare accession. The amplification sizes of markers are indicated in Fig. S4 in Additional file 3. c A dot plot showing the Blastn alignment result of an O. rufipogon gene (CU406257) to a contig (OsIPC11280438) of the indica dispensable genome