Gossypium stocksii (E1) genome ZSTU_v1

We used a hybrid strategy of genome sequencing and assembly in this work. Briefly, Pacbio long reads (102.8×) and Illumina short reads (123.5×) were used for contig construction, which gave rise to a total of 173 contigs (Figure 1b). These contigs were anchored and ordered using Hi-C data, resulting in a chromosomal-level genome of 127 scaffolds. The assembled genome is about 1.45 Gb in length, with about 99.2% accounting for 13 pseudochromosomes that are ranged from 83.8 to 129.5 Mb. BUSCO and CEGMA evaluation indicated the assembly’s completeness was about 95.4–98.4%, while 98.7% of the generated short reads could be mapped to the genome (coverage 99.9%). During the preparation of this manuscript, another genome assembly of G. stocksii was built towards a comprehensive understanding of G. stocksii resistance to CLCuD (Grover et al., 2021). Grover’s assembly shows comparable quality to our assembly. One of the main differences between the two projects is the strategy of gene annotation, i.e. Grover et al. used a series of RNA-seq data from closely related species to assist the gene modelling and annotation. In contrast, we used the transcripts generated from four G. stocksii tissues (leaf, stem, root and flower) by RNA-seq (one library for each tissue, 6.8–9.5 Gb) and Iso-seq (one library for mixed tissues, 28.9 Gb). Eventually, this work identified a total of 46 224 protein-coding genes, one-third more than that of Grover’s assembly. 

Publication: Yu, et al. Multi-omics assisted identification of the key and species-specific regulatory components of drought-tolerant mechanisms in Gossypium stocksii. Plant biotechnology journal. 2021, 19:1690–1692. doi: 10.1111/pbi.13655