Diploid, allopolyploid and haploid cotton sequencing

We generated sequencing data from parental diploids A2 and D5, their synthetic F1 (A2 x D5), two natural allopolyploids AD1 and AD2, as well as their derived haploids, hAD1 by the GhDMP knock-out system and hAD2 through semigamy. By including the haploid lines of allopolyploids into transcriptomic comparisons between diploid and polyploid cottons, we aimed to isolate the immediate effects of genome doubling, in reverse through haploid induction, from the long-term consequences of natural allopolyploidization. This approach allowed us to resolve the transcriptomic consequences of allopolyploidization at a finer resolution.