Gossypium hirsutum (AD1) 'TX-1000' genome CRI_v1

Three allotetraploid cotton genomes (Gossypium ekmanianum [(AD)6, Ge], Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp].) were sequenced and assembled using a combination of sequencing technologies, including single-molecule realtime (PacBio), paired-end Illumina sequencing, and chromatin conformation capture (Hi-C). An initial assembly was generated via FALCON (22) using at least 20.83 million PacBio long reads for each cotton species and subsequently corrected using Illumina paired-end data (average 120-fold coverage). These megabase assemblies (N50 of 1.57, 1.23, and 11.49 Mb for Ge, Gs, and Ghp, respectively) were combined with Hi-C interaction information to produce chromosome-scale scaffolds, yielding final assemblies of 2.34, 2.29, and 2.29 Gb for Ge, Gs, and Ghp, respectively. These high-quality assemblies had scaffold N50 values of more than 107 Mb (Table 1), with 99% of bases anchored onto chromosomes and with 99% of mapped Illumina reads covering about 97% of the genomes.  Nearly all of the 1,614 Embryophyta benchmarking universal single-copy orthologs (BUSCOs, embryophyta_odb10) were complete in the Ge (99.2%), Gs (97.4%), and Ghp (99.3%) assemblies and the long terminal repeat (LTR) assembly index (LAI score 13.7 in Ge, 12.8 in Gs, and 12.7 in Ghp) further indicated that these three assemblies could be considered "reference quality".

Table 1: Features of three tetraploid cotton assemblies