Summary The diploid wild cotton species Gossypium australe possesses excellent traits including resistance to disease and delayed gland morphogenesis, and has been successfully used for distant breeding programmes to incorporate disease resistance traits into domesticated cotton. Here, we sequenced the G. australe genome by integrating PacBio, Illumina short read, BioNano (DLS) and Hi‐C technologies, and acquired a high‐quality reference genome with a contig N50 of 1.83 Mb and a scaffold N50 of 143.60 Mb. We found that 73.5% of the G. australe genome is composed of various repeat sequences, differing from those of G. arboreum (85.39%), G. hirsutum (69.86%) and G. barbadense (69.83%). The G. australe genome showed closer collinear relationships with the genome of G. arboreum than G. raimondii and has undergone less extensive genome reorganization than the G. arboreum genome. Selection signature and transcriptomics analyses implicated multiple genes in disease resistance responses, including GauCCD7 and GauCBP1, and experiments revealed induction of both genes by Verticillium dahliae and by the plant hormones strigolactone (GR24), salicylic acid (SA) and methyl jasmonate (MeJA). Experiments using a Verticillium‐resistant domesticated G. barbadense cultivar confirmed that knockdown of the homologues of these genes caused a significant reduction in resistance against Verticillium dahliae. Moreover, knockdown of a newly identified gland‐associated gene GauGRAS1 caused a glandless phenotype in partial tissues using G. australe. The G. australe genome represents a valuable resource for cotton research and distant relative breeding as well as for understanding the evolutionary history of crop genomes.

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We cloned the GbABR1 gene from highly resistant Gossypium barbadense Xinhai15 based on the candidate genes screened by transcriptome sequencing that were related to resistance to Verticillium wilt. A sequence characteristic analysis showed that GbABR1 was an ERF subfamily B4 member and was a new member of the AP2 family of sea-island cotton. The GbABR1 gene was expressed highly in roots compared with the levels in leaves and stems in cotton. Expression was enhanced significantly in cotton after infection by Verticillium dahliae, indicating that GbABR1 probably plays an important role in the response to biotic stress. The results of subcellular localisation showed that GFP:GbABR1 was localised to the nucleus. GbABR1 silencing via the virus-induced gene silencing (VIGS) method indicated that the incidence of disease and the disease index in VIGS-silenced plants were much higher than in the control after infection by Verticillium dahliae. The GbABR1-overexpressing Arabidopsis plants showed similar resistance to Verticillium dahliae compared to the wild type. These results indicate that the GbABR1 gene plays a positive role in resistance to Verticillium wilt. The GbABR1-overexpressing Arabidopsis plants presented dwarfism, early maturation and early bolting compared with wild-type plants, suggesting that GbABR1 also participates in growth and development.

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