Table 4. Homoeolog-specific bias in developing cotton fiber.

	Total # genesa	At = Dt	At>Dt	At<Dt	Total biased genes (%)
Entire data
wild 10 dpa	18,315	13,815	2,258	2,242	4,500 (24.6%)
wild 20 dpa	19,163	14,941	2,141	2,081	4,222 (22.0%)
dom 10 dpa	17,551	11,641	2,966	2,944	5,910 (33.7%)
dom 20 dpa	15,901	13,126	1,382	1,393	2,775 (17.5%)
DE genes during development
wild 10 dpa	2,315	1,335	468	512	980 (42.3%)
wild 20 dpa	2,612	1,632	490	490	980 (37.5%)
dom 10 dpa	626	291	163	172	335 (53.5%)
dom 20 dpa	693	422	131	140	271 (39.1%)
DE genes during domestication
wild 10 dpa	1,691	1,256	223	212	435 (25.7%)
dom 10 dpa	1,605	1,066	289	250	539 (33.6%)
wild 20 dpa	951	567	183	201	384 (40.4%)
dom 20 dpa	631	360	131	140	271 (42.9%)

A_t = A-homoeolog; D_t = D-homoeolog; A_t = D_t, equal expression of homoeologs; A_t>D_t, biased expression of the A_t homoeolog; A_t<D_t, biased expression of the D_t homoeolog; DE = differential expression from the contrasts of development (10 vs. 20 dpa) or domestication (wild vs. dom).

^a includes genes having at least RPKM≧1 in either A or D-homoeolog specific reads across all biological replicates.