Approved strains of kiwifruit bacterial canker pathogens

In many kiwifruit-producing countries including Japan, bacterial canker disease has become a serious problem, causing major damage. The causal bacterium (Pseudomonas syringae pv. actinidiae) is now classified into five biovars (biovars 1, 2, 3, 5 and 6) based on the differences in various phenotypes and genotypes. In addition, it is becoming clear that repertories of pathogenicity-related genes and virulence toward kiwifruit differ among biovars. Of these, four biovars (biovars 1, 3, 5 and 6) have been confirmed to exist in Japan, causing canker disease on Actinidia chinensis, A. deliciosa and A. arguta.

The NARO Genebank has a lot of strains belonging to the four biovars confirmed to exist in Japan. They were characterized based on phenotypic tests, PCR assays, MLSA and comparative genome analyses, showing that some biovars have extremely rich variation and can be subdivided into several groups. Therefore, for each biovar/group, we chose some strains with typical characteristics as the approved strains and decided to show them here with related information.

  • Reference Sawada, H. and Fujikawa, T. (2019). Genetic diversity of Pseudomonas syringae pv. actinidiae, pathogen of kiwifruit bacterial canker. Plant Pathology 68: 1235-1248. [10.1111/ppa.13040]
  • Reference Fujikawa, T. and Sawada, H. (2019). Genome analysis of Pseudomonas syringae pv. actinidiae biovar 6, which produces the phytotoxins, phaseolotoxin and coronatine. Sci. Rep. 9: 3836. [10.1038/s41598-019-40754-9]
  • Reference Fujikawa, T. and Sawada, H. (2016). Genome analysis of the kiwifruit canker pathogen Pseudomonas syringae pv. actinidiae biovar 5. Sci. Rep. 6: 21399. [10.1038/srep21399]
  • Reference Genka, H., Baba, T., Tsuda, M., Kanaya, S., Mori, H., Yoshida, T., Noguchi, M.T., Tsuchiya, K. and Sawada, H. (2006). Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars. J. Mol. Evol. 63: 401-414. [10.1007/s00239-005-0271-4]
  • Reference Sawada, H., Takeuchi, T. and Matsuda, I. (1997). Comparative analysis of Pseudomonas syringae pv. actinidiae and pv. phaseolicola based on phaseolotoxin-resistant ornithine carbamoyltransferase gene (argK) and 16S-23S rRNA intergenic spacer sequences. Appl. Environ. Microbiol. 63: 282-288. [10.1128/aem.63.1.282-288.1997]
Approved strains of kiwifruit bacterial canker pathogens
MAFF No.BiovarTox
Island*1
Phaseolotoxin
Production*2
Coronatine
Biosynthesis
Gene Cluster*3
Pac_ICE
1, 2 or 3*4
Gene RegionGenome DataDistribution
'211985biovar 1++--16S acnB cts gapA gyrB pfk pgi rpoDSMHD00000000Order
'302145biovar 1++--16S acnB cts gapA gyrB pfk pgi rpoDJAAEYG000000000Order
'613024biovar 1++--16S acnB cts gapA gyrB pfk pgi rpoDJAAEYH000000000Order
'302133biovar 1++--16S acnB cts gapA gyrB pfk pgi rpoDJAAEYI000000000Order
'211981biovar 1+---16S acnB cts gapA gyrB pfk pgi rpoDJAAEYJ000000000Order
'211983biovar 1+---16S acnB cts gapA gyrB pfk pgi rpoDJAAEYF000000000Order
'302091biovar 1+---16S acnB cts gapA gyrB pfk pgi rpoDJAAEYK000000000Order
'613017biovar 1----16S acnB cts gapA gyrB pfk pgi rpoDJAAEYL000000000Order
'613018biovar 1----16S acnB cts gapA gyrB pfk pgi rpoDJAAEYM000000000Order
'212324biovar 1----16S acnB cts gapA gyrB pfk pgi rpoDJAAEYN000000000Order
'212101biovar 3---Pac_ICE116S acnB cts gapA gyrB pfk pgi rpoDPGSP00000000Order
'212104biovar 3---Pac_ICE116S acnB cts gapA gyrB pfk pgi rpoDPGSX00000000Order
'212109biovar 3---Pac_ICE116S acnB cts gapA gyrB pfk pgi rpoDPGSS00000000Order
'212145biovar 3---Pac_ICE116S acnB cts gapA gyrB pfk pgi rpoDPGSV00000000Order
'212357biovar 3---Pac_ICE116S acnB cts gapA gyrB pfk pgi rpoDPGSZ00000000Order
'212115biovar 3----16S acnB cts gapA gyrB pfk pgi rpoDPGSO00000000Order
'212118biovar 3----16S acnB cts gapA gyrB pfk pgi rpoDPHQZ00000000Order
'212056biovar 5----16S acnB cts gapA gyrB pfk pgi rpoDBBWG00000000Order
'212061biovar 5----16S acnB cts gapA gyrB pfk pgi rpoDNKQU00000000Order
'212054biovar 5----16S acnB cts gapA gyrB pfk pgi rpoDPESZ00000000Order
'212057biovar 5----16S acnB cts gapA gyrB pfk pgi rpoDJAAEYO000000000Order
'212063biovar 5----16S acnB cts gapA gyrB pfk pgi rpoDCP024712 CP024713 CP024714Order
'212134biovar 6+++-16S acnB cts gapA gyrB pfk pgi rpoDMSBW00000000Order
'212141biovar 6+++-16S acnB cts gapA gyrB pfk pgi rpoDMSBX00000000Order
'212133biovar 6+++-16S acnB cts gapA gyrB pfk pgi rpoDPVZI00000000Order
'212137biovar 6+++-16S acnB cts gapA gyrB pfk pgi rpoDPVZJ00000000Order
'212138biovar 6+++-16S acnB cts gapA gyrB pfk pgi rpoDPVZL00000000Order
  • *1 The presence or absence of tox island [genomic island containing phaseolotoxin biosynthesis gene cluster (argK-tox cluster)] was investigated with PCR assays targeting argK, argD, desI and amtA and with genome analyses.
  • *2 Phaseolotoxin production was confirmed by means of growth inhibition assays using sensitive Escherichia coli strains.
  • *3 The presence or absence of coronatine biosynthesis gene cluster was investigated with PCR assays targeting cfl, corR and cmaU and with genome analyses.
  • *4 The presence or absence of Pac_ICE1, Pac_ICE2 and Pac_ICE3 was investigated with PCR assays targeting the respective internal regions and with genome analyses.