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Table 2 Variations within genes between G. thurberi and G. davidsonii genomes

From: Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

Variation type Syntenic region SV region
Number Ratio Number Ratio
Structurally conserved genes a 24,094 75.58 729 66.03
Without amino acid substitutions b 2832 8.88 88 7.97
No DNA variation in CDS region 699 2.19 22 1.99
No DNA variation in CDS and intron region 292 0.92 10 0.91
No DNA variation in genic region c 4 0.01 0 0.00
Same sense mutation 2133 6.69 66 5.98
With amino acid changes d 21,262 66.70 641 58.06
With missense mutation in CDS 17,488 54.86 532 48.19
With 3n InDel in CDS 3774 11.84 109 9.87
Genes with large-effect mutations e 2915 9.14 126 11.41
With 3n ± 1 InDel in CDS 1035 3.25 32 2.90
Start-codon mutation 694 2.18 29 2.63
Stop-codon mutation 641 2.01 31 2.81
Splice-acceptor mutation 32 0.10 0 0.00
Splice-donor mutation 513 1.61 34 3.08
Genes with large structural variations f 4868 15.27 249 22.55
At least one CDS missing 4145 13.00 209 18.93
Total 32,981g 100.00 1104g 100.00
  1. a Structurally conserved genes, including genes without amino acid substitutions (b) and with amino acid changes (d). b Genes without amino acid substitutions (no DNA variation in the CDS region or intron regions). c Genic regions including 2 kb upstream and downstream of the gene body. d Genes with amino acid changes, including missense mutations in the CDS region and with 3n InDels in the CDS region. e Genes with large-effect mutations, including 3n ± 1 InDels in the CDS region, start-codon mutations, stop-codon mutations, splice-acceptor mutations, and splice-donor mutations. f Genes with large structural variations, including at least one CDS missing or other structural variation. g The total number of genes included for the analysis (genes and their orthologs in the counterpart genome, anchored on the 13 chromosomes)