Estimation of variance of two cotton diploid transcriptomes. (A) Redundancy of ESTs in A- and D-genome species. Using self-BLASTN analysis (e-value < e-100), redundant ESTs (either isoforms or paralogs) were identified. (B) Frequency distribution of Ks for orthologous and paralogous gene pairs between GaA, GrD, and JGI-D sequences. (C) Specificity of cotton A and D transcriptomes. Reciprocal BLASTN analyses were performed between GaA and GrD assemblies. The cut-off e-value for uniqune and shared genes was e-10.