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Fig. 1 | Genome Biology

Fig. 1

From: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

Fig. 1

Population structure and genetic diversity in G. hirsutum and G. barbadense accessions. a The unweighted neighbor-joining phylogenetic tree of 1913 cotton accessions was constructed based on 20,000 random SNPs from core SNPs. The G. tomentosum (AD3), G. mustelinum (AD4), G. darwinii (AD5), G. ekmanianum (AD6), G. stephensii (AD7) of tetraploid species, G. arboreum (A2) and G. davidsonii (D3-d) of diploid species serve as outgroup. b Principal component analysis (PCA) plot of the first two components for all accessions. c STRUCTURE analysis of all cotton accessions with different numbers of clusters K = 6 and K = 12 (K = 12 is optimal value). The x-axis lists the outgroup species (gray), G. barbadense (blue), G. hirsutum landrace accessions (orange), and G. hirsutum improved accessions (green) respectively, and the y-axis quantifies genetic diversity in each accession. The other structure results are shown in the Additional file 2: Figure S2. d Nucleotide diversity (π) and fixation index divergence (Fst) across the five groups. e The number of deletions, duplications, inversions, and translocations in five populations (two-sided Wilcoxon rank-sum test for adjacent groups, P < 0.001). Each node represents one accession. In this analysis, the number of SVs was shown with the TM-1 reference genome

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