Background Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that impact gene manifestation and morphology. suitability of cotton for cultivation worldwide. These resources should facilitate epigenetic executive, breeding, and improvement of polyploid plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1229-8) contains supplementary material, which is available to authorized users. gametes between varieties or by interspecific hybridization followed by genome doubling [3, 8]. Genomic relationships in the polyploids can induce genetic and epigenetic changes including DNA methylation [1, 3]. DNA methylation changes can produce meiotically stable epialleles [9, 10] which are transmissible through natural selection and breeding. For example, stable DNA methylation in promoters can be inherited as epialleles, which confer symmetric blossom development in  and quantitative trait loci of colorless non-ripening and vitamin E content material in tomato [12, 13]. In vegetation, DNA methylation happens in CG, CHG, and CHH (H?=?A, T, or C) contexts through distinct pathways . In ((, and lead to lethality in rice . DNA methylation is also responsible for seed development  and Thiamet G adaptation to environments . Furthermore, DNA methylation changes are associated with manifestation of homoeologous genes in resynthesized and natural allotetraploids [26C28], natural allopolyploids , and paleopolyploid beans . However, epigenomic resources in polyploids are very limited, and the practical part of epialleles in morphological development and crop domestication remains mainly unfamiliar. Cotton is the largest source of renewable textile dietary fiber and an excellent model for studying Thiamet G polyploid development and crop domestication [31, 32]. Allotetraploid cotton was created approximately 1C 1.5 million years ago (MYA)  by interspecific hybridization between two diploid species, one having the A genome like in (Ga, A2) and (A1), and the other resembling the D5 genome found in extant species (Gr); divergence of A-genome and D-genome ancestors is definitely estimated at ~6 MYA (Fig.?1a). The allotetraploid diverged into five or more varieties [32, 34]. Two of them, (Gh, Upland cotton) and (Gb, Pima cotton), were individually domesticated for higher dietary fiber yield and wider geographical distribution; these characteristics were accompanied by remarkable morphological changes including loss of photoperiod level of sensitivity, reduction in seed dormancy, and conversion from tree-like crazy species to an annual crop [31, 33, 35]. Fig. 1 Evolution of DNA methylation and genome sequence during polyploidization in cotton. a Allotetraploid cotton ((((A2), diploid (D5), their interspecific hybrid (A2D5), wild allotetraploid (wGh), wild allotetraploid (wGb), allotetraploid (Gt), allotetraploid (Gm), allotetraploid (Gd), cultivated allotetraploid (cGh), and cultivated allotetraploid (cGb) (Fig.?1a; Additional file 1: Table S1). To exclude the effect of nucleotide variation across species (especially between C and T) on DNA methylation analysis, we identified 352,667,453 conserved cytosines (~48% of the total cytosines of the genome) between all species and present in two biological replicates for further analysis (Additional file 2: Physique S1). Among them, 12,045,718 (~3.4% of) differentially methylated cytosines (DmCs) were found across all species; there were more DmCs between diploid cottons and tetraploid cottons (diploid vs. tetraploid) than for other comparisons (diploid vs. diploid cottons, wild tetraploid vs. wild tetraploid, and wild vs. cultivated cottons) (Fig.?1b). Methylation divergent levels at CG and non-CG sites, respectively, that were conserved among all species (Additional file 2: Physique S1) were used to generate neighbor-joining phylogenetic trees. Phylogenetic trees with CG and non-CG sites recapitulated the known evolutionary associations of cotton species , including sister taxa associations between and and between and (Fig.?1c; Additional file 2: Physique S2). This suggests concerted evolution between DNA sequence and methylation changes. Gene-body methylated genes occur largely in CG sites  and evolve slowly . To test the relationship between methylation and sequence evolution in genic regions, we divided orthologous genes into CG body-methylated (value peaks at 0.007C0.034) (Fig.?1d), suggesting that this methylation change rate is faster than the neutral sequence substitution rate. In the CG body-unmethylated genes, although Thiamet G the sequence variation remained at a similar level, the methylation peak disappeared (Fig.?1e). DNA methylation divergence between progenitor-like FGF18 diploid species TEs are often associated with DNA methylation and genome complexity [14, 38, 39]. In diploid species, the genome is usually twofold larger and.