Fig. 1

Prediction of genes encoding secreted proteins and their distribution on the chromosomes in the genome of cotton cultivar Zhongzhimian No.2 (ZZM2). A Characteristics of predicted secreted proteins and their corresponding gene distribution on the 26 chromosomes in the cotton genome. The density data were calculated by the number of encoded genes using step windows (window = 500 kb, walking step = 100 kb). Secreted proteins were predicted as those with signal peptide (SP), lack of the transmembrane (TM) domain, and the extracellular location. The transmembrane domain was predicted by two tools, TMHMM2.0 [55] and Phobius [56]. The subcellular location of the prediction of secreted proteins was carried out using the plant model of the WolfPsort procedure by (circle e) [54], and the predicted localization during the host–pathogen interaction was predicted using the fungi model (circle g–i). A01–A13 and D01–D13 represent the 13 chromosomes of the A sub-genome and the D sub-genome of the ZMM2 genome, respectively. B Ratio of secreted proteins encoded in each chromosome versus the total number of secreted proteins. The statistic of the encoded genes in the genome was set as the comparison group. C Comparison of the gene density between the encoded putative secreted proteins and total encoded proteins by step windows. Step window: window = 500 kb, walking step = 100 kb. The top panel represents the ratio that the gene density of encoded secreted proteins versus the gene density of total encoded proteins. D Prediction of the localization of the secretome during host–pathogen interactions using the fungi model of WolfPsort [54]