Gossypium barbadense (AD2) 'Pima90' genome HEAU_v1

We assembled 2.29 Gb and 2.21 Gb of the NDM8 and Pima90 genomes, respectively (Table 1). To accomplish this, we obtained 205.18 Gb and 200.62 Gb long reads of NDM8 and Pima90 genomes, respectively, representing 180.38-fold coverage depth in total on the basis of single-molecule real-time (SMRT) sequencing. The initial assembly corrected by Illumina paired-end data (233.75-fold coverage in total) resulted in contigs with an N50 size of 15.28 Mb for NDM8 and 9.65 Mb for Pima90. Subsequently, these corrected contigs were connected to 754 superscaffolds for NDM8 and 909 for Pima90 using a total of 232.90-fold 10x Genomics linked-read data. Finally, we constructed chromosome-scale scaffolds using more than 125-fold Hi-C interacting unique paired-end data from each cotton genome. The final assemblies included 353 scaffolds for NDM8 and 309 for Pima90, resulting in contig and scaffold N50 values of 13.15 Mb and 107.67 Mb for NDM8 and 9.24 Mb and 102.45 Mb for Pima90. A total of 99.57% and 99.75% of genomes were anchored onto pseudochromosomes in NDM8 and Pima90, respectively, and the very few gaps (0.003% in NDM8 and 0.06% in Pima90) indicated the contiguity of the sequences. High mapping ratios (99.16% in the two genomes) and low error assembly site ratios (1.87 × 10−7 in NDM8 and 2.95 × 10−7 in Pima90) indicated the accuracy of the genomes. Besides, 96.1% and 95.9% of 1,440 embryophyta Benchmarking Universal Single-Copy Orthologs (BUSCOs) present in NDM8 and Pima90, respectively, showed the integrity of the genomes.

Table 1. Global summary of the final genome assemblies for NDM8 and Pima90

Publication: Ma, et al. High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nature Genetics 53:1385–1391 (2021)