Gossypium hirsutum (AD1) 'YM11' genome XAAS_v1

To characterize genomes corresponding to upland cotton with cold tolerance features that are suitable for the Xinjiang climate, YM11, an accession with elite cold tolerance and adaptation to the climate of Xinjiang, was selected for genome de novo assembly.  The sprouted seeds of YM11 (pure lines) were uniformly planted in seedling trays and then placed in a greenhouse at a 12 h/12 h day/night regime, 32 ◦C/27 ◦C accordingly. The planting medium was a mixture of peat soil, perlite, and vermiculite at a ratio of 3:1:1. During the three-leaf stage, the seedlings were uniformly placed in an artificial climate chamber at 4 ◦C with a light-to-dark cycle of 14 h:10 h and illumination intensity of 1500~2000 lx for cold stress treatment. The sampling time was set at 0 h and 6 h. Transcriptome sequencing (RNA-seq) and metabolome analysis were performed at the two-time points with three and six biological replicates, respectively. Approximately 2 g of leaves from each biological replicate were frozen in liquid nitrogen immediately, ground into fine powder, and then transferred to a -80 ◦C refrigerator for storage. In particular, two replicated samples (~1 g) at both 0 h and 6 h from the same tissue used in RNA-seq were selected for the CUT&Tag assay. In addition, approximately 5 g young leaves of YM11 were sampled to extract genomic DNA for genome assembly, and a collection of YM11 root, stem, leaf, flower, and boll mixed samples from the field was used to conduct RNA-seq for transcriptome-assisted genome annotation.

Global statistics of the genome assembly of YM11.