Figure 3: Evolution of gene models, DNA fragments and syntenic blocks among G. hirsutum (AtDt) and two diploid cotton genomes, G. arboreum (A) and G. raimondii (D).
(a) Scenarios and statistics of gene conservation. Solid lines indicate currently observed genes, and dotted lines indicate lost genes. The numbers beneath each drawing represent the number of gene pairs found in the three different genomes that fit the specific model. From left to right, genes present in all four genomes, genes not observed in At, genes not observed in Dt, genes not observed in either A or At, genes not observed in either D or Dt, genes not observed in A, genes not observed in D. (b) HE of genomic segments between the At and Dt subgenomes in a region of G. hirsutum chromosome 9 (Gh9). The curves in the upper panel show homologous gene pairs between At and A or At and D. The lower panel shows the Ks value distribution for syntenic blocks, which indicates HE in the tetraploid cotton. The dot plots show distribution of Ks values and the boxplots display variations of Ks values between A and D genomes. Note that some of the dots (outliers) are not included in the boxplots due to their low probabilities. (c) Distribution of Ks values between four cotton genomes and T. cacao (upper panel) and single-nucleotide variation (SNV) rate (lower panel) among different cotton genomes.
