Abstract
A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA). The disease was first reported in China and Japan in the 1980s. A severe outbreak of PSA began in Italy in 2008 and has spread to other European countries. PSA was found in both New Zealand and Chile in 2010. To study the evolution of the pathogen and analyse the transmission of PSA between countries, genomes of strains from China and Japan (where the genus Actinidia is endemic), Italy, New Zealand and Chile were sequenced. The genomes of PSA strains are very similar. However, all strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish them from all other PSA strains. Similarly, all the PSA strains from the 2008 Italian outbreak form a distinct clonal group and those from Chile form a third group. In addition to the rare SNPs present in the core genomes, there is abundant genetic diversity in a genomic island that is part of the accessory genome. The island from several Chinese strains is almost identical to the island present in the New Zealand strains. The island from a different Chinese strain is identical to the island present in the strains from the recent Italian outbreak. The Chilean strains of PSA carry a third variant of this island. These genomic islands are integrative conjugative elements (ICEs). Sequencing of these ICEs provides evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas syringae to PSA. The analyses of the core genome SNPs and the ICEs, combined with disease history, all support the hypothesis of an independent Chinese origin for both the Italian and the New Zealand outbreaks and suggest the Chilean strains also originate from China.
Highlights
Pseudomonas syringae pv. actinidiae (PSA) was first isolated and described in Japan in 1989 as the causal agent of bacterial canker of kiwifruit (Actinidia deliciosa) [1]
Strains and Genomes In the present study, we were especially interested in analysing the genomes of PSA strains from the outbreak in New Zealand, and if possible, tracing the origin of this outbreak
We sequenced the genomes of four New Zealand PSA strains involved in serious damage to kiwifruit vines, two strains from Shaanxi province in China isolated in 2010 (M7 and M228), one strain isolated in Italy in 2010, two strains from Chile and a strain from Japan, isolated in 1984 (Table 1)
Summary
Pseudomonas syringae pv. actinidiae (PSA) was first isolated and described in Japan in 1989 as the causal agent of bacterial canker of kiwifruit (Actinidia deliciosa) [1]. Actinidiae (PSA) was first isolated and described in Japan in 1989 as the causal agent of bacterial canker of kiwifruit (Actinidia deliciosa) [1]. A similar disease was described in 1989 in Sichuan Province of China [3] and subsequently in the Chinese provinces of Anhui, and Shaanxi (references cited in [4]). The first report from Europe was in Italy in 1992 [6]; this was followed by a more severe outbreak of bacterial canker in 2008 [7]. By 2010 the disease had spread to Portugal and France on both the green kiwifruit A. deliciosa and the gold kiwifruit A. chinensis [8,9]. In October 2010 (spring), bacterial canker of kiwifruit was found in Te Puke in New Zealand [10]. The outbreak has since spread from the Te Puke region PSA has been found in Chile, in late 2010 [11]
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