Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum

Abstract

Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called TAL (transcription activator-like) effectors, which induce susceptibility genes in the host’s cells. To gain further insight into the global diversity of the pathogen, to elucidate their repertoires of TAL effector genes and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.

Evaluation Methods, Resistant Germplasm, and Breeding for Resistance to Bacterial Blight in Cotton: A Review

“…DNA polymorphisms can occur due to mutations, such as nucleotide modifications, insertions, and deletions. To date, draft genomes of Xcm from several races, including races 1, 2, 3, 12, 18, and 20, a highly virulent strain, a local strain of unnamed race (likely race 18) in Mississippi, and three African Xcm strains, have been published (Cunnac et al, 2013;Pérez-Quintero et al, 2023;Phillips et al, 2017;Showmaker et al, 2017;Wheeler et al, 2022;Zhai et al, 2013). The genome sequences allowed the development of a TaqMan-based qPCR method to detect and differentiate five Xcm races (1, 2, 3, 12, and 18) in cotton leaves and seeds (Wang et al, 2019).…”