Fig. 1

Overviews of C. japonica (cjaND) reference genome and construction of the genetic linkage map. a An overall photograph of the cjaND tree used for genome sequencing. The close-up photos of flowers, seeds, and fruits are on the right. b Circular representation of the assembled cjaND genome features. Different layers of circles are listed as follows: (1) the pseudo-molecules of chromosomes; (2–9) the distribution of GC, repetitive elements, gene models, noncoding RNAs, microRNAs, rRNA, snoRNA and tRNA; (10) the syntenic regions within the cjaND genome. For details of setting the Circos plot, see the supplementary files. The genome of cjaND has high levels of retrotransposons (c) and DNA transposons (d), which are classified based on the sequence similarity search. e Scatter plot of gene length and exon number based on the genome annotation of cjaND