Table 1. Accession information used in this study and the number and percentage of short reads mapped onto the Cotton D genome reference assembly.
| Species | Origin | Stage | Total Reads | Mapped Reads (%) |
| G. hirsutum var. yucatanense (TX2090) | Yucatan, Mexico | 10 dpa 20 dpa | 9,598,358 10,517,180 | 7,554,107 (78.7) 8,175,498 (77.7) |
| G. hirsutum var. yucatanense (TX2094) | Yucatan, Mexico | 10 dpa 20 dpa | 11,139,818 14,110,893 | 8,326,479 (74.7) 10,627,792 (75.3) |
| G. hirsutum var. yucatanense (TX2094 = YUC*) | Yucatan, Mexico | 10 dpa 20 dpa | 10,444,338 10,991,115 | 8,908,976 (85.3) 7,851,707 (71.4) |
| G. hirsutum var. yucatanense (TX2095) | Yucatan, Mexico | 10 dpa 20 dpa | 42,989,086 15,142,099 | 33,550,251 (78.0) 11,646,705 (76.9) |
| G. hirsutum var. palmeri (TX665) | Yucatan, Mexico | 10 dpa 20 dpa | 14,559,567 29,461,705 | 11,627,366 (79.9) 23,229,997 (78.8) |
| G. hirsutum cv. Cascot L-7 | Plains in U.S.A | 10 dpa 20 dpa | 10,688,995 31,345,469 | 8,488,820 (79.4) 17,785,760 (56.7) |
| G. hirsutum cv. Coker 315 | Eastern U.S.A | 10 dpa 20 dpa | 14,201,314 10,615,133 | 11,065,757 (77.9) 5,881,452 (55.4) |
| G. hirsutum cv. CRB252† | Eastern U.S.A | 10 dpa 20 dpa | 9,986,108 8,344,787 | 7,583,439 (75.9) 4,720,388 (56.6) |
| G. hirsutum cv. Maxxa* | Western U.S.A | 10 dpa 20 dpa | 12,266,868 15,484,446 | 9,410,233 (76.7) 12,353,194 (79.8) |
| G. hirsutum cv. Texas Marker 1 (TM1) | Delta in U.S.A. | 10 dpa 20 dpa | 14,706,919 13,078,240 | 11,766,434 (80.0) 9,003,797 (68.8) |
CRB252-Derives from a double cross, SG 248/PHY 72//ST 474/Maxxa.
data from the study number SRP001603 at NCBI SRA. Fiber samples from TX2094 and Maxxa were collected in different growing seasons; thus, this TX2094 was noted as “YUC” to be distinguished from TX2094, which was collected in the same year as the other materials.