PROKARYOTES
crossm Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of Summer Canker in South Korea Sandra B. Visnovsky,a,d Preetinanda Panda,a,e Robert Taylor,b,d Andrew R. Pitmana,c,d The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealanda; Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealandb; Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealandc; Science Solutions for Better Border Biosecurityd‡; Scion, Rotorua, New Zealande
Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry.
ABSTRACT
P
ectobacterium carotovorum subsp. actinidiae has been reported as the causal agent of canker-like symptoms of kiwifruit species Actinidia chinensis in South Korea (1). Canker symptoms caused by P. carotovorum subsp. actinidiae are similar to those presented by kiwifruit infected with Pseudomonas syringae pv. actinidiae biovar 3, a pandemic lineage that has had a deleterious effect on kiwifruit production worldwide (2). However, the canker caused by P. carotovorum subsp. actinidiae seems to appear only under conditions of high humidity in the summer season, with the pathogen requiring higher temperatures (~30 to 32°C) to cause disease and not producing the leaf spots characteristic of P. syringae pv. actinidiae (1). We announce here the draft genome sequences of P. carotovorum subsp. actinidiae ICMP 19971 (OHJ3) and ICMP 19972 (SYJ3), isolated from yellow kiwifruit Actinidia chinensis cv. Hort 16A cane cankers extruding red rust ooze in South Korea (1), which were obtained from the International Collection of Microorganisms from Plants (ICMP) (http://www.landcareresearch.co.nz/ resources/collections/icmp). A comparison of the newly acquired P. carotovorum subsp. actinidiae genomes with the genomes of P. carotovorum subsp. actinidiae ICMP 19970 (KKH3) (accession no. NZ_JRMH00000000) and other pectobacteria, such as P. carotovorum subsp. brasiliensis, P. carotovorum subsp. carotovorum, Pectobacterium atrosepticum, and Pectobacterium wasabiae, will enable the taxonomic status of P. carotovorum subsp. actinidiae to be verified. Comparative analysis will also permit the identification of genetic traits associated with the capacity of P. carotovorum subsp. actinidiae to cause canker symptoms in kiwifruit plants, which could subsequently be used for risk-based diagnostics and risk assessments of similar exotic organisms at the New Zealand border. Volume 5 Issue 14 e00104-17
Received 1 February 2017 Accepted 7 February 2017 Published 6 April 2017 Citation Visnovsky SB, Panda P, Taylor R, Pitman AR. 2017. Draft genome sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, two strains isolated from Actinidia chinensis with symptoms of summer canker in South Korea. Genome Announc 5:e00104-17. https:// doi.org/10.1128/genomeA.00104-17. Copyright © 2017 Visnovsky et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Sandra B. Visnovsky, [email protected]. ‡ For this virtual institution, see http://www.b3nz.org.
genomea.asm.org 1
Visnovsky et al.
Pure cultures of P. carotovorum subsp. actinidiae strains ICMP 19971 and ICMP 19972 were incubated overnight in lysogeny broth medium at 28°C. Genomic DNA was isolated using a DNeasy blood and tissue kit (Qiagen). DNA samples of good quality were sequenced to generate 100-bp Illumina paired-end reads using an Illumina HiSeq 4000 system (Beijing Genomics Institute, Hong Kong). The quality of the sequence reads was checked using FastQC (Babraham Bioinformatics, United Kingdom), and low-quality reads (score of ⬍Q30) were trimmed using Fastq-Mcf (3). The remaining sequence reads were assembled into contigs using SOAPdenovo version 2.04 (4), and the contigs were aligned with the reference P. carotovorum subsp. actinidiae genome with accession no. ALIU00000000 using the SOAPaligner version 2.21 (5, 6) to generate a draft genome sequence for both ICMP 19971 and ICMP 19972. Coding sequences for each isolate were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The estimated draft genome sizes for ICMP 19971 and ICMP 19972 were 4,891,911 and 4,886,946 bp, respectively. They comprised 50 and 49 scaffolds, respectively, with both genomes having a 51.53% G⫹C content. The PGAP annotations for each genome predicted 4,171 coding sequences for ICMP 19971 and 4,201 coding sequences for ICMP 19972. A number of loci were identified as common to the two P. carotovorum subsp. actinidiae strains and other bacteria that cause diseases of woody plants, suggesting they may be required for pathogenicity of P. carotovorum subsp. actinidiae on kiwifruit. A detailed assessment of the genetic traits shared by ICMP 19971, ICMP 19972, and the previously sequenced P. carotovorum subsp. actinidiae strain ICMP 19970 will follow. Accession number(s). The draft genome sequences of ICMP 19971 and ICMP 19972 are available in the GenBank database under accession numbers MPUI00000000 and MPUJ00000000, respectively. The versions described in this paper are the first versions. ACKNOWLEDGMENTS This work was funded by Plant and Food Research Ltd. as part of the Better Border Biosecurity programme (B3) (http://www.b3nz.org) and by Zespri International Ltd.
REFERENCES 1. Koh Y, Kim G, Lee Y, Sohn S, Koh H, Kwon S, Heu S, Jung J. 2012. Pectobacterium carotovorum subsp. actinidiae subsp. nov., a new bacterial pathogen causing canker-like symptoms in yellow kiwifruit, Actinidia chinensis. N Z J Crop Hort Sci 40:269 –279. https://doi.org/10.1080/ 01140671.2012.707129. 2. McCann HC, Rikkerink EH, Bertels F, Fiers M, Lu A, Rees-George J, Andersen MT, Gleave AP, Haubold B, Wohlers MW, Guttman DS, Wang PW, Straub C, Vanneste JL, Rainey PB, Templeton MD. 2013. Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLoS Pathog 9:e1003503. https://doi.org/10.1371/journal.ppat.1003503. 3. Aronesty E. 2011. Ea-utils: “command-line tools for processing biological sequencing data.” https://expressionanalysis.github.io/ea-utils/.
Volume 5 Issue 14 e00104-17
4. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient shortread de novo assembler. GigaScience 1:18. https://doi.org/10.1186/2047 -217X-1-18. 5. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966 –1967. https://doi.org/10.1093/bioinformatics/btp336. 6. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124 –1132. https://doi.org/10.1101/gr.088013.108.
genomea.asm.org 2
crossm Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of Summer Canker in South Korea Sandra B. Visnovsky,a,d Preetinanda Panda,a,e Robert Taylor,b,d Andrew R. Pitmana,c,d The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealanda; Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealandb; Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealandc; Science Solutions for Better Border Biosecurityd‡; Scion, Rotorua, New Zealande
Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry.
ABSTRACT
P
ectobacterium carotovorum subsp. actinidiae has been reported as the causal agent of canker-like symptoms of kiwifruit species Actinidia chinensis in South Korea (1). Canker symptoms caused by P. carotovorum subsp. actinidiae are similar to those presented by kiwifruit infected with Pseudomonas syringae pv. actinidiae biovar 3, a pandemic lineage that has had a deleterious effect on kiwifruit production worldwide (2). However, the canker caused by P. carotovorum subsp. actinidiae seems to appear only under conditions of high humidity in the summer season, with the pathogen requiring higher temperatures (~30 to 32°C) to cause disease and not producing the leaf spots characteristic of P. syringae pv. actinidiae (1). We announce here the draft genome sequences of P. carotovorum subsp. actinidiae ICMP 19971 (OHJ3) and ICMP 19972 (SYJ3), isolated from yellow kiwifruit Actinidia chinensis cv. Hort 16A cane cankers extruding red rust ooze in South Korea (1), which were obtained from the International Collection of Microorganisms from Plants (ICMP) (http://www.landcareresearch.co.nz/ resources/collections/icmp). A comparison of the newly acquired P. carotovorum subsp. actinidiae genomes with the genomes of P. carotovorum subsp. actinidiae ICMP 19970 (KKH3) (accession no. NZ_JRMH00000000) and other pectobacteria, such as P. carotovorum subsp. brasiliensis, P. carotovorum subsp. carotovorum, Pectobacterium atrosepticum, and Pectobacterium wasabiae, will enable the taxonomic status of P. carotovorum subsp. actinidiae to be verified. Comparative analysis will also permit the identification of genetic traits associated with the capacity of P. carotovorum subsp. actinidiae to cause canker symptoms in kiwifruit plants, which could subsequently be used for risk-based diagnostics and risk assessments of similar exotic organisms at the New Zealand border. Volume 5 Issue 14 e00104-17
Received 1 February 2017 Accepted 7 February 2017 Published 6 April 2017 Citation Visnovsky SB, Panda P, Taylor R, Pitman AR. 2017. Draft genome sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, two strains isolated from Actinidia chinensis with symptoms of summer canker in South Korea. Genome Announc 5:e00104-17. https:// doi.org/10.1128/genomeA.00104-17. Copyright © 2017 Visnovsky et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Sandra B. Visnovsky, [email protected]. ‡ For this virtual institution, see http://www.b3nz.org.
genomea.asm.org 1
Visnovsky et al.
Pure cultures of P. carotovorum subsp. actinidiae strains ICMP 19971 and ICMP 19972 were incubated overnight in lysogeny broth medium at 28°C. Genomic DNA was isolated using a DNeasy blood and tissue kit (Qiagen). DNA samples of good quality were sequenced to generate 100-bp Illumina paired-end reads using an Illumina HiSeq 4000 system (Beijing Genomics Institute, Hong Kong). The quality of the sequence reads was checked using FastQC (Babraham Bioinformatics, United Kingdom), and low-quality reads (score of ⬍Q30) were trimmed using Fastq-Mcf (3). The remaining sequence reads were assembled into contigs using SOAPdenovo version 2.04 (4), and the contigs were aligned with the reference P. carotovorum subsp. actinidiae genome with accession no. ALIU00000000 using the SOAPaligner version 2.21 (5, 6) to generate a draft genome sequence for both ICMP 19971 and ICMP 19972. Coding sequences for each isolate were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The estimated draft genome sizes for ICMP 19971 and ICMP 19972 were 4,891,911 and 4,886,946 bp, respectively. They comprised 50 and 49 scaffolds, respectively, with both genomes having a 51.53% G⫹C content. The PGAP annotations for each genome predicted 4,171 coding sequences for ICMP 19971 and 4,201 coding sequences for ICMP 19972. A number of loci were identified as common to the two P. carotovorum subsp. actinidiae strains and other bacteria that cause diseases of woody plants, suggesting they may be required for pathogenicity of P. carotovorum subsp. actinidiae on kiwifruit. A detailed assessment of the genetic traits shared by ICMP 19971, ICMP 19972, and the previously sequenced P. carotovorum subsp. actinidiae strain ICMP 19970 will follow. Accession number(s). The draft genome sequences of ICMP 19971 and ICMP 19972 are available in the GenBank database under accession numbers MPUI00000000 and MPUJ00000000, respectively. The versions described in this paper are the first versions. ACKNOWLEDGMENTS This work was funded by Plant and Food Research Ltd. as part of the Better Border Biosecurity programme (B3) (http://www.b3nz.org) and by Zespri International Ltd.
REFERENCES 1. Koh Y, Kim G, Lee Y, Sohn S, Koh H, Kwon S, Heu S, Jung J. 2012. Pectobacterium carotovorum subsp. actinidiae subsp. nov., a new bacterial pathogen causing canker-like symptoms in yellow kiwifruit, Actinidia chinensis. N Z J Crop Hort Sci 40:269 –279. https://doi.org/10.1080/ 01140671.2012.707129. 2. McCann HC, Rikkerink EH, Bertels F, Fiers M, Lu A, Rees-George J, Andersen MT, Gleave AP, Haubold B, Wohlers MW, Guttman DS, Wang PW, Straub C, Vanneste JL, Rainey PB, Templeton MD. 2013. Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLoS Pathog 9:e1003503. https://doi.org/10.1371/journal.ppat.1003503. 3. Aronesty E. 2011. Ea-utils: “command-line tools for processing biological sequencing data.” https://expressionanalysis.github.io/ea-utils/.
Volume 5 Issue 14 e00104-17
4. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient shortread de novo assembler. GigaScience 1:18. https://doi.org/10.1186/2047 -217X-1-18. 5. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966 –1967. https://doi.org/10.1093/bioinformatics/btp336. 6. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124 –1132. https://doi.org/10.1101/gr.088013.108.
genomea.asm.org 2
