Fig. 2

Conservation of the cotton secretome in cultivar Zhongzhimian No.2 (ZZM2). A Comparison of the protein properties of the predicted secretome versus the total encoded proteins in the ZZM2 genome. The length ratio of CDS/gene represents the value of coding sequence length compared to the gene length; the value of the gene without intron is 1.0. Asterisks (***) represent statistical significance at P < 0.001 based on unpaired Student’s t-tests, and Levene’s test was used to assess the homogeneity of variances. B Synteny analysis of encoded secreted proteins from the D05 chromosome with those of the other 25 chromosomes. The synteny relationship was constructed by ortholog clustering (both coverage and identities up to 30%) of secreted proteins from the D05 chromosome with other secreted proteins from the other 25 chromosomes, present in blue lines. The red lines represent the self-orthologs of secreted proteins within the D05 chromosome. The outer circle with green blocks represents the 26 chromosomes of the ZZM2 genome, and the inner circle with brown lines represents the secreted proteins encoded in the ZZM2 genome. C Matrix representing the gene number of each chromosome with ortholog relationships of the 26 chromosomes. The data in columns but not in rows represent the gene number of each chromosome (top labels) in ortholog clustering (both coverage and identities up to 30%) with the other chromosomes (left labels). D Sequence divergence of orthologs detected under different ortholog clustering parameters. The ortholog number was determined by the ortholog clustering with 30% parameters, and the attenuation of total gene numbers among these orthologs was investigated under the 50% and 70% parameters. High variation represents the total gene numbers attenuated from 30 to 50 and 70%, medium variation represents the total gene numbers attenuated from 30 to 50 or 70%, and low variation represents identical sequence under 30%, 50%, and 70% parameters