Table 1.

Gene Features Predicted Along Homoeologous A_T and D_T BACs Surrounding the CesA1 Gene in Allopolyploid Cotton

		Length (bp)^b				Total length, exons^b				Total length, introns			Length (a.a.)
Gene	Putative function^a	D_T	A_T	Exons	D_T	A_T	Introns	D_T	A_T	D_T	A_T	K_s	K_a	K_sil
1	ABC transporter^d	244	244	*	244	244	*	0	0	81	81	0.035	0.000	0.035
2	GTP-binding protein	1909	1925	2	657	657	1	1252	1268	218	218	0.054	0.006	0.047
3	WRKY TF	1024	1013	3	822	819	2	202	194	273	274	0.064	0.014	0.041
4	Arabidopsis hypothetical protein	994	992	3	471	471	2	523	521	156	156	0.020	0.017	0.061
5	No BLAST homoeology	519	519	1	519	519	0	0	0	172	172	0.084	0.026	0.084
6	G-protein B	2376	2376	9	1068	1068	8	1308	1308	355	355	0.043	0.012	0.029
7	CesA	4080	4083	12	2925	2925	11	1155	1158	974	974	0.041	0.004	0.033
8	LeuRR	1308	1308	1	1308	1308	0	0	0	435	435	0.020	0.012	0.020
9	PRR/Se-binding protein	2628	2628	3	2418	2418	2	210	210	805	805	0.019	0.013	0.018
10	Ribosomal protein L11	1273	1275	4	519	519	3	754	756	172	172	0.008	0.000	0.029
11	LeuRR transmembrane or kinase	3189	3197	11	1857	1857	10	1332	1340	618	618	0.042	0.006	0.031
12	Growth regulator	2631	2637	10	1797	1800	9	834	837	598	599	0.050	0.015	0.037
13	Permease	2633	2629	13	1575	1575	12	1058	1054	524	524	0.016	0.006	0.021
14	Arabidopsis expressed protein	4349	4325	8	1287	1278	7	3062	3047	425	422	0.037	0.014	0.029
										Weighted average			0.037	0.010	0.032

↵a Putative function is assigned by BLAST homoeology to genes in GenBank. The locations of genes along the BAC contigs are represented in Figure 2.
↵b Total length including stop codon.
↵c K_s, K_a, and K_sil denote rate of substitution across all sites, substitutions at nonsynonymous sites, and synonymous sites within codons plus all noncoding positions, respectively.
↵d This predicted gene is fragmented in the BAC; a start codon was identified, but no intronic sequences or stop codon was found. This gene would presumably be full length, were it not fragmented in the generation of the BAC library. An asterisk (*) signifies that the number of exons and introns is not known.

Incongruent Patterns of Local and Global Genome Size Evolution in Cotton