Gossypium hirsutum (AD1) 'EM22' genome HAU v1.0

We constructed an introgression line population between G. hirsutum Emian22, a high-yield cultivar with moderate fiber quality, and G. barbadense 3–79, a genetic standard with superior fiber. Introgression between these two species is of great interest due to their complementary properties (i.e., yield and fiber quality) whose genetic underpinnings may be elucidated by evaluating introgression populations. To explore regulatory perturbations of gene expression caused by introgression, we generated a genome assembly for the recipient (Emian22) genome of the IL population to improve the accuracy of genetic analysis, and performed direct genomic comparisons with the donor parent (3-79). We generated 1284 fiber transcriptome datasets for developing cotton fiber samples from 323 different introgression lines using 4 fiber developmental timepoints (5 days post-anthesis (DPA), 10 DPA, 15 DPA and 20 DPA). These timepoints encompass primary cell wall synthesis and the transition to secondary wall synthesis. We developed a multi-locus model method to estimate additive and dominant effects simultaneously, to identify genetic associations between introgression segments and gene expression, as well as with fiber quality-related traits. This study thus presents a comprehensive depiction of genome-wide regulatory perturbations in gene expression caused by interspecific introgression, a topic of general interest with respect to speciation, but also of importance to agronomic traits in a major crop.

We de novo assembled the genome of G. hirsutum Emian22, resulting in a final genome assembly of 2.24 gigabase pairs (Gb), with a contig N50 of 11.14 Mb and scaffold N50 of 97.54 Mb. About 99.94% of the 2.24 Gb assembled genome was oriented and organized into 26 pseudochromosomes. Benchmarking Universal Single-Copy Orthologue (BUSCO, 98.70% of the 1614 core eukaryotic genes) analysis indicated the high completeness and contiguity of the assembled genome. The assessment of the LTR Assembly Index (LAI) and the assembly of centromeres also suggest high completeness, contiguity, and correctness of the Emian22 genome. We predicted a total of 76102 protein-coding genes in the Emian22 genome, 95.02% of which were subjected to functional annotation.

Publication: Chen, X., Hu, X., Li, G., et al. (2024). Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton. Advanced Science, 11(40), 2401549.