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.