Cotton Genomics and Genetics 2025, Vol.16, No.5, 210-221 http://cropscipublisher.com/index.php/cgg 213 private genes that only exist in certain materials. These seemingly marginal genes are actually often related to differences in plants' responses to adverse conditions, their adaptability to the environment, or regulatory mechanisms. In other words, those genes that we originally thought were unimportant have instead become the key to enhancing the resistance and breeding potential of cotton. Their value is far greater than initially thought. Figure 1 Sequencing features of five cotton allotetraploid species (Adopted from Chen et al., 2020) Image caption: a, Evolution and domestication of five polyploid lineages, Gh, Gb, Gt, Gd and Gm, after polyploidization between an A-genome African species (Ga-like) and a D-genome American species (Gr-like). Typical seeds from each species are shown. The divergence time estimates are based on 21 567 single orthologs among the 5 species by using the synonymous substitution rate (r) of 3.48 × 10-9. Scale bar, 10 mm; ka, thousand years ago. b, Chromosomal features and synteny of the Gm genome. Notes in circos plots: (i) estimated lengths of 13 A and 13 D homoeologous pseudochromosomes; (ii) distribution of annotated genes; (iii) TE content (Gypsy, steel blue; Copia, grey; other repeats, orange); (iv,v) stacked SNP (iv) and indel (v) densities between Gm and Gb, Gd, Gh and Gt, respectively (see inset), and (vi) syntenic blocks between the homoeologous A and D chromosomes. The densities in plots in (ii)-(v) are represented in 1 Mb with overlapping 200-kb sliding windows. c, Genome-wide syntenic relationships among A and D subgenomes in five allotetraploids relative to the A-genome-like Ga (A2 genome) and D-genome-like Gr (D5 genome). Structural variations among syntenic blocks are marked with colored ribbons (Adopted from Chen et al., 2020)
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