The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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Comparative Genome Analysis Reveals Natural Variations in the Genomes of Erwinia pyrifoliae, a Black Shoot Blight Pathogen in Apple and Pear

  • Lee, Gyu Min (School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Ko, Seyoung (School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Oh, Eom-Ji (Graduate School of Biotechnology, Kyung Hee University) ;
  • Song, Yu-Rim (Department of Horticultural Biotechnology, Kyung Hee University) ;
  • Kim, Donghyuk (School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Oh, Chang-Sik (Graduate School of Biotechnology, Kyung Hee University)
  • Received : 2020.06.06
  • Accepted : 2020.09.07
  • Published : 2020.10.01
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Abstract

Erwinia pyrifoliae is a Gram-negative bacterial plant pathogen that causes black shoot blight in apple and pear. Although earlier studies reported the genome comparison of Erwinia species, E. pyrifoliae strains for such analysis were isolated in 1996. In 2014, the strain E. pyrifoliae EpK1/15 was newly isolated in the apple tree showing black shoot blight in South Korea. This study aimed to better understand the similarities and differences caused by natural variations at the genomic level between newly isolated E. pyrifoliae EpK1/15 and the strain Ep1/96, which were isolated almost 20 years apart. Several comparative genomic analyses were conducted, and Clusters of Orthologous Groups of proteins (COG) database was used to classify functional annotation for each strain. E. pyrifoliae EpK1/15 had similarities with the Ep1/96 strain in stress-related genes, Tn3 transposase of insertion sequences, type III secretion systems, and small RNAs. The most remarkable difference to emerge from this comparison was that although the draft genome of E. pyrifoliae EpK1/15 was almost conserved, Epk1/15 strain had at least three sorts of structural variations in functional annotation according to COG database; chromosome inversion, translocation, and duplication. These results indicate that E. pyrifoliae species has gone natural variations within almost 20 years at the genomic level, and we can trace their similarities and differences with comparative genomic analysis.

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References

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