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Draft genome sequence of a bacterial plant pathogen Erwinia pyrifoliae strain EpK1/15 isolated from an apple twig showing black shoot blight
Korean J. Microbiol 2018;54(1):69-70
Published online March 31, 2018
© 2018 The Microbiological Society of Korea.

Gyu Min Lee1, Eom-Ji Oh2, Seyoung Ko1, Jungkum Park2, Duck Hwan Park3, Donghyuk Kim1,*, and Chang-Sik Oh2,*

1Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea,
2Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea,
3Applied Biology Program, Division of Bioresource Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
Correspondence to: (D. Kim) E-mail: donghyuk.kim@khu.ac.kr; Tel.: +82-31-201-2683; Fax: +82-31-203-4969 / (C.S. Oh) E-mail: co35@khu.ac.kr; Tel.: +82-31-201-2678; Fax: +82-31-204-8116
Received November 7, 2017; Revised December 22, 2017; Accepted December 29, 2017.
Abstract

Erwinia pyrifoliae is a Gram-negative bacterium causing black shoot blight in apple and Asian pear trees. E. pyrifoliae strain EpK1/15 was isolated in 2014 from an apple twig from the Pocheon, Gyeonggi-do, South Korea. In this study, we report the draft genome sequence of E. pyrifoliae EpK1/15 using PacBio RS II platform. The draft genome is comprised of a circular chromosome with 4,027,225 bp and 53.4% G + C content and a plasmid with 48,456 bp and 50.3% G + C content. The draft genome includes 3,798 protein-coding genes, 22 rRNA genes, 77 tRNA genes, 13 non-coding RNA genes, and 231 pseudo genes.

Keywords : Erwinia pyrifoliae, apple, black shoot blight, draft genome sequence, PacBio RS II
Body

Erwinia pyrifoliae is primarily a bacterial pathogen of Asian or Nashi pear (Pyrus pyrifolia), causing black shoot blight and has been reported only in Korea and Japan since 1990’s (Rhim et al., 1999; Kim et al., 1999; McGhee et al., 2002; Geider et al., 2009). Disease symptoms caused by this pathogen are very similar to fire blight caused by E. amylovora, which is widely distributed worldwide (van der Zwet et al., 2012). E. pyrifoliae belongs to the Enterobacteriaceae, which is a large family of Gram-negative, facultative anaerobe (Octavia et al., 2014). To date, the complete genome sequences of E. pyrifoliae strains Ep1/96 and DSM12163 isolated in 1996 in South Korea have been reported (Kube et al., 2010; Smits et al., 2010). In this study, the new strain EpK1/15 (KACC 19528) was isolated from an apple twig showing black shoot blight in Pocheon, Gyeonggi-do, South Korea in 2014. To further understand the differences between E. pyrifoliae strains that were isolated with a few decades’ interval, we present here the draft genome sequence of E. pyrifoliae EpK1/15.

Total genomic DNA of E. pyrifoliae EpK1/15 was extracted with the DNeasy Blood & Tissue Kit (Qiagen), and the extracted DNA was used to generate 20 kb SMRTbellTM template libraries. Genome sequencing was performed at ChunLab, Inc. using the Pacific Biosciences RSII sequencing method. The sequencing depth was 272.82 × coverage of the genome, and the sequence was assembled de novo into 2 contigs with the PacBio SMRT Analysis pipeline version 2.3.0. Genes in the resulting draft genome sequence were annotated with the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The draft genome of EpK1/15 consists of one chromosome with 4,027,225 bp (53.4% G + C content) and one circular plasmid with 48,456 bp (50.3% G + C content). A total of 3,798 protein-coding genes, 22 rRNA genes (5S, 23S, and 16S), 77 tRNA genes, 13 non-coding RNA, and 231 pseudo genes were predicted. It carries one intact hrp gene cluster to form a Hrp type III secretion system and to encode important effector genes, dspA/E and eopB, and two harpin genes, hrpN and hrpW, in its chromosome for virulence in host plants. Interestingly, the plasmid in EpK1/15 strain is larger than the largest plasmids in both Ep1/96 and DSM12163 and also three small plasmids reported in Ep1/96 and DSM12163 strains were missing in this draft genome sequence of EpK1/16 strain. Because E. pyrifoliae strain EpK1/15 was isolated 20 years later than the first sequenced strain Ep1/96, further in-depth comparative analysis of the EpK1/15 genome would provide insights on the evolution of E. pyrifoliae species in field conditions.

Genome features of Erwinia pyrifoliae EpK1/15

Genomic featuresChromosomePlasmid
Genome size (bp)4,027,22548,456
G + C content (%)53.450.3
Total genes3,85654
Protein-coding genes3,74454
rRNA genes (5S, 23S, 16S)22 (8, 7, 7)0
tRNA genes770
Non-coding RNA genes130
Pseudo genes22110

Nucleotide sequence accession numbers

The draft genome sequences of a chromosome and a plasmid of E. pyrifoliae strain EpK1/15 have been deposited in the GenBank database under accession numbers CP023567 (chromosome) and CP023568 (plasmid), respectively.

적요

Erwinia pyrifoliae는 그람 음성 세균으로 사과와 배에 가지검은마름병을 일으킨다. E. pyrifoliae EpK1/15 균주가 병징을 보이는 경기도 포천지역의 사과나무 가지에서 2014년도에 분리되었다. 본 논문에서는 PacBio RS II 플랫폼을 이용하여 E. pyrifoliae EpK1/15 균주의 전체 유전체를 분석하여 보고한다. 본 균주는 G + C 비율이 53.4%이며, 4,027,225 bp로 구성된 염색체와 G + C 비율이 50.3%이며, 48,456 bp로 구성된 plasmid를 지니고 있다. 이들 염색체와 plasmid DNA에서 3,798개의 단백질 코딩 유전자, 22개의 rRNA, 77개의 tRNA, 13개의 non-coding RNA 및 231개의 위유전자(pseudo gene)가 확인되었다.

Acknowledgements

This work was supported by the “Cooperative Research Program for Agriculture Science & Technology Development (Project No: PJ0117582017)” of the Rural Development Administration, Republic of Korea.

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