Figure Legends
Figure 1. A picture of Cheilinus underlatus used for the genome sequencing
Figure 2. Chromosome size and gene density ofCheilinus underlatus . Genes were plotted in 100 kb windows, and chromosomes size was showed on the left axis in Mb.
Figure 3. Gene annotation and length distribution forCheilinus undulatus . (A) Gene annotated in the public databases. (B) Comparison of gene, exon, and intron length distributions between C. undulatus and other six species.
Figure 4 . Express of genes based on the transcriptome of Cheilinus underlatus . (A) Numbers of the expressed genes muscle shared, and tissue-specific expressed genes.(B) Different express of genes in tissue and muscle used as background. mu: muscle; re: retina; li: liver; or: olfactory organ; br: brain; sp: spleen; gl: gonad.
Figure 5 . Divergence and percentage of transposons in the genome of Cheilinus underlatus . (A)Divergence distribution of known transposons in C. underlatus .(B) Pie charts comparing the percentage of transposons presented in a genome. The area of the pie chart noted genome size.
Figure 6. Phylogenetic tree, divergence time and gene families of Cheilinus underlatus . (A) Gene family comparison among C. undulatus and other fishes, and single-copy orthologs were used to construct phylogenetic tree.(B) The phylogenetic relationship of C. underlatus with other fishes. The red blot in the internal nodes indicated fossil calibration times. All nodes had support values of 100%. Numbers under each species showed gene families that have been expanded (green) and contracted (red) since the split of species from the most recent common ancestor. The numbers near each node correspond to the estimated divergence time of these species. The circled number on the right is the same as picture.
Figure 7. Opsin gene synteny and orientation in genomes from species tree based on 619 single-copy orthologs . (A) synteny of SWS2 and LWS1opsin genes in 13 reprsentative species andCallorhinchus milii used as outgroup. (B) synteny of Rh2 opsin gene in species the same as that of the left. The genomic location of each synteny is summarized in Table S1. The files of the genome annotations could be used in Table S2.
Figure 8. Gene conversions of Rh2 opsin, transposons and genes distribution . (A) Gene conversion analyses by sliding window. Pairwise rate of synonymous substitutions between Rh2 copies calculated with a window of 30 and a step size of 1, and vertical dotted lines depicted significantly positive selection sites of Rh2 opsin with P<0.05. (B) The numbers in transposons and genes distribution along positive/negative strands in Chromosome 3. The vertical dotted lines depicted locations of opsin genes. X axis depicted a 100 kb window, and transposon numbers in Y axis have been divided by 10.