Fig. 2.

Gene family expansion among 11 cotton species. a Genomic landscape between G. thurberi and G. davidsonii genomes. (i) Genomes of G. thurberi (right panel) and G. davidsonii (left panel). (ii,iii) Transposable elements and gene density. (iv) 5mC DNA methylation levels. (v) 6mA DNA methylation levels. (vi) A and B compartments across the chromosome, orange indicates A compartments and blue indicates B compartments. (vii) Expression level based on RNA-seq analysis of leaves. The expression level was normalized by the number of reads per bin/(number of mapped read (in millions))×bin length (kb). (viii) InDel density between G. thurberi and G. davidsonii. (ix) SNP density between G. thurberi and G. davidsonii. (x) PAV density between G. thurberi and G. davidsonii. (xi) Syntenic block between G. thurberi and G. davidsonii. All data in panel (i)-(x) are shown in 500-kb windows. b A phylogenetic tree based on 7561 single-copy genes. The ratios of gene expansion and contraction of each branch are showed in the pie diagrams. The digits present the number of gene families which have experienced expansion or contractions. c,d KEGG pathway enrichment of the gene families which have experienced expansion or contraction in G. thurberi and G. davidsonii