Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis

Abstract

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.

Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. Chow (Orchidaceae)

“…Furthermore, lots of DEGs were markedly enriched into plant hormone signal transduction pathway. Consistently, it has been reported that auxin [74,75], cytokinins [76,77], ethylene [75,[78][79][80], gibberellin [81], abscisic acid [75,82,83], brassinosteroids [80], salicylic acid [75,78,84], jasmonic acid [75,78,[84][85][86], strigolactones [87] can actively participate in disease response. Among them, salicylic acid signal transduction and jasmonic acid/ethylene signal transduction are considered as the most common plant hormone signal transduction pathways in response to biological or abiotic stress.…”

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

“…Very recently, Udall et al reported the de novo assembly of the genome of G. raimondii and its close relative Gossypium turneri using PacBio long reads, Hi-C, and Bionano optical mapping technologies, which helped to correct some minor assembly errors in previous version of the G. raimondii genome assembly [21]. Using the same strategy, another group published a draft genome of a disease-resistant species Gossypium australe with a contig N50 of 1.83 Mb [22]. In addition, high-resolution transcriptional landscape of G. arboreum is also available [23].…”

Molecular cloning and characterization of GhERF105, a gene participated in the regulation of gland formation from cotton (Gossypium hirsutum L.)

“…Silencing GauGRAS1 by VIGS leads to glandless stems and petiole and didn't change the form of glands in the leaves in G. australe. Moreover, the gossypol content in the stem of the GauGRAS1silenced plants was signi cantly reduced [38]. However, the molecular mechanism for pigment gland formation remains complicated and unclear, which has limited progress in low-gossypol breeding of cotton.…”

“…CGP1 (Cotton Gland Pigmentation 1), which interacted with GoPGF, was identi ed through comparative transcriptome analysis of glanded and glandless cotton accessions and was involved in the regulation of gossypol biosynthesis but not gland formation [36]. In addition, the novel RanBP2 zinc nger protein (ZFP) and GauGRAS1, which played the roles in the development of the cotton gland, were identi ed using suppression subtractive hybridization (SSH) from upland cotton 'Xiangmian 18' [9,[37][38][39]. During the past three decades, there has been some progress in the molecular mechanism of gland formation and the relationship between gossypol and pigment gland.…”