Abstract
For decades, Xanthomonas vasicola pv. musacearum (Xvm) has been an economically important bacterial pathogen on enset in Ethiopia. Since 2001, Xvm has also been responsible for significant losses to banana crops in several East and Central African countries, with devastating consequences for smallholder farmers. Understanding the genetic diversity within Xvm populations is essential for the smart design of transnationally reasoned, durable, and effective management practices. Previous studies have revealed limited genetic diversity in Xvm, with East African isolates from banana each falling into one of two closely related clades previously designated as sublineages SL 1 and SL 2, the former of which had also been detected on banana and enset in Ethiopia. Given the presumed origin of Xvm in Ethiopia, we hypothesized that both clades might be found in that country, along with additional genotypes not seen in Central and East African bananas. Genotyping of 97 isolates and whole‐genome sequencing of 15 isolates revealed not only the presence of SL 2 in Ethiopia, but additional diversity beyond SL 1 and SL 2 in four new clades. Moreover, SL 2 was detected in the Democratic Republic of Congo, where previously SL 1 was the only clade reported. These results demonstrate a greater range of genetic diversity among Xvm isolates than previously reported, especially in Ethiopia, and further support the hypothesis that the East/Central Africa xanthomonas wilt epidemic has been caused by a restricted set of genotypes drawn from a highly diverse pathogen pool in Ethiopia.
Highlights
Within the γ-proteobacteria, the genus Xanthomonas consists of more than 20 species and over 100 different pathovars causing several economically important diseases of plants (Vauterin et al, 1995)
Xanthomonas vasicola pv. musacearum (Xvm) was initially described in Ethiopia on Ensete ventricosum (Castellani, 1939; Yirgou & Bradbury, 1968) and subsequently on banana (Yirgou & Bradbury, 1974) as Xanthomonas musacearum
The reference study of Wasukira et al (2012) described two sublineages within Xvm—one being hypothesized from Ethiopia (SL 1) and one of unknown origin (SL 2)—and proposed a list of diagnostic single-nucleotide polymorphism (SNP)
Summary
Within the γ-proteobacteria, the genus Xanthomonas consists of more than 20 species and over 100 different pathovars causing several economically important diseases of plants (Vauterin et al, 1995) Among these pathogens is Xanthomonas vasicola pv. If Ethiopia were the centre of origin, it should harbour an even greater genetic diversity of Xvm in addition to the two previously known clades. To test this hypothesis, we genotyped a large collection of isolates from a range of geographical locations in Ethiopia and Central and East Africa, using eight single-nucleotide polymorphisms (SNPs) previously reported to distinguish SL 1 from SL 2 (Wasukira et al, 2012). We sequenced the genomes of 15 Xvm isolates representing the full range of haplotypes, and carried out a phylogenetic reconstruction from genome-wide data
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