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

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

Variation type	Syntenic region		SV region
Variation type	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	32,981^g	100.00	1104^g	100.00

^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)

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