The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility

Abstract

Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (G. davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid.

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

“…This BUSCO recovery is similar to recent publications of other diploid cotton genomes (Huang et al, 2020, Grover et al, 2020Grover et al, 2021. Annotation of the genome produced 39,100 unique genes, similar to the previously published cotton diploids (Paterson et al 2012;Li et al 2014;Du et al 2018;Udall et al 2019;Grover et al 2020Grover et al , 2021cGrover et al , 2021bHuang et al 2020). The annotation of A1-Wagad contained ~5000 fewer unique genes than the published annotation for A1-africanum, possibly due to annotation methods and/or filtering.…”

Recent progression and future perspectives in cotton genomic breeding

“…The assembly length of the latest version of the G. babardense genome is 2,210 Mb with a contig N50 of 9.24 Mb (Ma et al, 2021b). Genomes for G. anomalum (B 1 ) (Grover et al, 2021a; Xu et al, 2022), G. australe (G 2 ) (Cai et al, 2020), G. bickii (G 1 ) (Sheng et al, 2022), G. ekmanianum and G. stephensill (Peng et al, 2022), G. rotundifolium (K 2 ) (Wang et al, 2021b), and G. stocksii (E 1 ) (Grover et al, 2021b), were also sequenced and successfully assembled. These cotton genome sequences have the potential to provide powerful genomic markers and target genes for genomic selection in cotton.…”

Molecular evolution following allopolyploidization in Gossypium

“…anomalum (Grover et al 2021a)), D (G. turneri ) and G. raimondii ), E (G. stocksii (Grover et al 2021b)), F (G. longicalyx (Grover et al 2020)), G (G. australe (Cai et al 2020)), and K (G. rotundifolium (Wang et al 2021)).…”