Figure Legends
Figure 1. The Hi-C heatmap, karyotypes, and exon length of the male O. bidens . (A) A Heat map generated by Hi-C technology presented contact matrices of thirty-eight chromosomes. The color bar indicates the logarithm of the strength of the contact density. (B) The karyotypes of male O. bidens ’ genome. (C) The distributions of gene exon length in male O. bidens ’ genome.
Figure 2. Gene annotation and function of male O. bidens’ genome . (A) Different databases annotated genes. (B) Gene functionally classification by GO analysis. (C) A Venn diagram showing the number of species-specific and shared gene orthogroups of O. bidens betweenD. rerio , L. rohita , C. carpio, and A. graham .
Figure 3. A phylogenetic tree based on single-copy genes from the nine genome sequences . (A) The number of orthologous for nine fish species. Names for species are abbreviated to Ag, Anabarilius grahami ; Cc, Cyprinus carpio ; Dr, Danio rerio ; Ga,Gasterosteus aculeatus ; Lr, Labeo rohita ; Ob,Opsariichthys bidens ; Ol, Oryzias latipes ; Sr,Sinocyclocheilus rhinocerous ; Tr, Takifugu rubripes . (B) A bayesian phylogenetic tree, gene families, and divergence time of maleO. bidens . The bayesian posterior probability and the maximum likelihood bootstrap had support values of 100%. The numbers upper the lines indicate gene families expansions (+ and red) and contractions (- and green).
Figure 4. GnRH signaling pathway of male O. bidens’ genome . The gene-marked colors indicated the gene copy number presented on this signaling pathway (KEGG ID: ko04912).
Figure 5. Physical distribution of GnRH signaling pathway expanded genes in male O. bidens’ genome . The gene-marked colors indicated gene expanded number (≥ 3, see Table S5 & S6).
Figure 6. Genomic comparisons between female and male O. bidens. Genomic comparisons of whole genome sequences directly, and the majority of female and male O. bidens chromosomes exhibited 1:1 correspondence except for chromosomes LG06 in male and GH14 and GH38 in female.
Figure 7 . Detail chromosome comparisons between LG06, GH14, and GH38, and structure variation between female and male O. bidens genomes . (A) The chromosome LG06 of male O. bidensgenome showed significant synteny with GH14 and GH38 of female O. bidens genome. (B) Statistics of the structural variations in various regions of the male genome by alignment with female O. bidensgenome.
Figure 8. Chromosome conserved synteny analysis between maleO. bidens and grass carp genome . (A) The chromosomes in the two genomes showed multiple chromosomes breaking off in grass carps corresponding to chromosomes in male O. bidens . (B) Detail inter-genomic conserved blocks with21,628 gene pairs between grass carp and male O. bidens genome.