Gossypium arboreum (A2) 'SXY1' genome HAU_v1

About the assembly

In this study, we applied Oxford Nanopore sequencing technology to assemble G. rotundifolium (K₂*) 'K201', G. arboreum (A₂) 'SXY1', and G. raimondii (D₅) 'D502' genomes. G. arboreum and G. raimondii genomes have been de novo assembled previously using Illumina and PacBio reads, but both genomes have a number of sequence gaps and require an improvement in assembly contiguity. We generated a total of 304 Gb, 212 Gb, 125 Gb Nanopore sequencing data with a genome coverage 124×, 131×, 167× for K₂*, A₂ and D₅, respectively. We assembled 3,593, 1,173 and 366 contigs for G. rotundifolium, G. arboreum and G. raimondii with a contig length of 2.44 Gb, 1.62 Gb and 0.75 Gb, respectively (Table 1). These initial contigs were polished using Illumina paired-end reads with a genome coverage of 108×, 118×, 132× for K₂*, A₂ and D₅. The contig N50 is 5.33 Mb, 11.69 Mb and 17.04 Mb for K₂*, A₂ and D₅, respectively. The maximum contig has a length of 32.72 Mb, 58.57 Mb and 43.74 Mb. After polishing contig using Illumina reads, we used high-through chromosome conformation capture (Hi-C) data to order and orient contigs, aimed at constructing pseudo chromosomes of each species. In the Hi-C assisted assembly, 2,559, 485 and 201 contigs were placed on the 13 chromosomes of K₂*, A₂ and D₅ genomes, occupying over 99% of genome length.

*Should be K₁₂

Table 1. Summary of genome assemblies and annotations of G. rotundifolium, G. arboreum and G.raimondii.

Supplementary Table 4. Comparing A2 genome with previously published genome version.

Publication

Wang, M. et al. Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton. Mol Biol Evol. 2021 May 11:msab128. doi: 10.1093/molbev/msab128.