Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1
© The Author(s). 2017
Received: 7 August 2017
Accepted: 5 December 2017
Published: 20 December 2017
Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot model strain isolated from a diseased potato tuber in the early 1980’s. The genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349 are protein coding and 102 are RNA genes.
Pectobacterium species are economically important plant pathogens that cause soft rot and blackleg disease on a range of plant species across the world [1, 2]. The main virulence mechanism employed by Pectobacterium is the secretion of vast amounts of plant cell wall-degrading enzymes [1, 3]. Due to their ability to effectively macerate plant tissue for acquisition of nutrients, Pectobacterium species are considered classical examples of necrotrophic plant pathogens. Among the Pectobacterium species, P. carotovorum has the widest host range while potato is the most important crop affected in temperate regions [1, 4]. P. carotovorum strain SCC1 was isolated from a diseased potato tuber in Finland in the early 1980’s . It is highly virulent on model plant hosts such as tobacco ( Nicotiana tabacum ) and thale cress ( Arabidopsis thaliana ) as well as on the original host, potato ( Solanum tuberosum ). For three decades, the strain has been used as a model strain in the study of virulence mechanisms of Pectobacterium as well as in the study of plant defense mechanisms against necrotrophic plant pathogens ([e.g. [6–13]). Here we describe the annotated genome sequence of P. carotovorum strain SCC1.
Classification and features
Classification and general features of Pectobacterium carotovorum strain SCC1 
Species Pectobacterium carotovorum
Strain: SCC1 (CFBP 8537)
Mesophile, able to grow at 37 °C
pH range; Optimum
Sucrose, lactose, melibiose, raffinose
Able to grow in 5% NaCl
60° 13′ 36.15” N
25° 00′ 54.77″ E
Genome sequencing information
Genome project history
P. carotovorum strain SCC1 has been used as a model soft rot pathogen in the field of plant-pathogen interactions ever since its isolation in the 1980’s. The sequencing of the genome of strain SCC1 was initiated in 2008 in order to further facilitate its use as a model pathogen.
One gap remaining, otherwise finished
Standard 454 and Solid libraries
454, SOLiD, Sanger
Chromosome 40×, plasmid 67×
gsAssembler v 1.1.03.24
Gene calling method
GenBank Date of Release
July 27, 2017
Source Material Identifier
Growth conditions and genomic DNA preparation
After isolation from potato in 1982, P. carotovorum strain SCC1 has been stored in 22% glycerol at −80 °C. For preparation of genomic DNA, the strain was first grown overnight on solid LB medium (10 g tryptone, 5 g yeast extract, 10 g NaCl, and 15 g agar per one liter of medium) at 28 °C. A single colony was then picked and grown overnight in 10 ml of liquid LB medium at 28 °C with shaking. Cells were harvested by centrifugation for 20 min at 3200 g at 4 °C and resuspended into TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA). SDS (5% w/v) and Proteinase K (1 mg/ml) were used to break the cells for one hour at 50 °C. Genomic DNA was extracted using phenol-chloroform purification followed by ethanol precipitation. The quantity and quality of the DNA was assessed by spectrophotometry and agarose gel electrophoresis.
Genome sequencing and assembly
Genome sequencing was performed at DNA and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Finland. Genomic DNA was sequenced using 454 (454 Life Sciences/Roche), SOLiD3 (Life Technologies) and ABI 3130xl Genetic Analyzer (Life Technologies) instruments. DNA was fragmented into approximate size of 800 bp using Nebulizer (Roche) followed by standard fragment 454 library with the GS FLX series reagents. For the SOLiD library genomic DNA was fragmented with a Covaris S2 Sonicator (Covaris Inc.) to approximate size of 250 bp. The library was prepared using the SOLiD library kit (Life technologies).Newbler (version 1.1) was used to assemble 366,453 pyrosequencing reads (77,6 Mbp) in approximate length of 240 bp with default settings into 100 large (>1000 bp) contigs. GAP4 program (Staden package) was used for contig editing, primer design for PCRs and primer walking, and finishing the genome. Gaps were closed using PCR and traditional primer walking Sanger sequencing method. Finally, SOLiD reads were mapped to the genome and fifteen single genomic positions were fixed. Final sequencing coverages were 40× in genome and 67× in plasmid sequences.
Coding sequences were predicted using the Prodigal gene prediction tool . GenePRIMP  was run to correct systematic errors made by Prodigal and to reanalyze the remaining intergenic regions for missed CDSs. Functional annotation for the predicted genes was performed using the PANNZER annotation tool . The annotation was manually curated with information from publications and the following databases: COG , KEGG , CDD , UniProt and NCBI non-redundant protein sequences. To identify RNA genes, RNAmmer v1.2  (rRNAs) and tRNAscan-SE  (tRNAs) were used. Clusters of Orthologous Groups assignments and Pfam domain predictions were done using the WebMGA server . Transmembrane helices were predicted with TMHMM  and Phobius . For signal peptide prediction, SignalP 4.1  was used. CRISPRFinder  was used to detect Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs).
Summary of P. carotovorum SCC1 genome: one chromosome and one plasmid
% of Total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
P. carotovorum strain SCC1 harbors a small cryptic plasmid of 5524 bp, pSCC1. The plasmid contains sequences for RNAI and RNAII, two non-coding RNAs involved in replication initiation and control in enterobacterial RNA priming plasmids such as ColE1 . A similar replication region has previously been described in the small cryptic plasmid pEC3 of P. carotovorum subsp. carotovorum strain IFO3380 . In addition to the two RNA genes, pSCC1 was predicted to contain nine protein-coding genes. Four of these (mobABCD) encode mobilization proteins. The mob locus is required for mobilization of non-self-transmissible plasmids and is found on many enterobacterial plasmids including pEC3 . No function could be assigned to the remaining five genes on pSCC1. One of them, SCC1_4463, is very similar to genes found in many Enterobacteriaceae genomes, especially those of genera Enterobacter , Escherichia and Salmonella , whereas similar genes to the other four on pSCC1 are not widely present in other sequenced genomes.
Pectobacterium infection is characterized by maceration symptoms caused by the secretion of a large arsenal of plant cell wall-degrading enzymes. Accordingly, the genome of P. carotovorum strain SCC1 was found to contain genes for eleven pectate lyases (pelABCILWXZ, hrpW, SCC1_1311, and SCC1_2381), one pectin lyase (pnl), four polygalacturonases (pehAKNX), one oligogalacturonate lyase (ogl), three cellulases (celSV, bcsZ), one rhamnogalacturonate lyase (rhiE), two pectin methylesterases (pemAB), and two pectin acetylesterases (paeXY). In addition, the genome harbors two genes encoding proteases previously characterized as plant cell wall-degrading enzymes (prt1, prtW) as well as a number of putative proteases, some of which may function in plant cell wall degradation. Different Pectobacterium species and strains have been found to harbor very similar collections of plant cell wall-degrading enzymes , and the number and types of enzymes in the genome of strain SCC1 fit this picture well.
Protein secretion plays an essential role in soft rot pathogenesis . The most important secretion system in Pectobacterium is the type II secretion system, also known as the Out system (outCDEFGHIJKLMN), which transports proteins from the periplasmic space into the extracellular environment . It is responsible for the secretion of most plant cell wall-degrading enzymes such as pectinases and cellulases as well as some other virulence factors such as the necrosis-inducing protein Nip [33, 35]. Furthermore, Pectobacterium genomes typically harbor multiple type I secretion systems, which secrete proteases and adhesins . At least four type I secretion systems are encoded in the genome of P. carotovorum SCC1 (prtDEF, SCC1_1144–1146, SCC1_1589–1591, and SCC1_3286–3288). Strain SCC1 also harbors a type III secretion system cluster (SCC1_2406–2432), which has previously been characterized in this strain and shown to affect the speed of symptom development during infection [6, 36]. Overall, the role of the type III secretion system in Pectobacterium is not well understood and P. wasabiae and P. parmentieri seem to lack it completely [32, 37]. The type IV secretion system has been shown to have a minor contribution to virulence of P. atrosepticum . However, it is sporadically distributed among Pectobacterium strains , and no type IV secretion genes could be found from the genome of P. carotovorum SCC1. Finally, the type VI secretion system has also been shown to have a small effect on virulence at least in some Pectobacterium species [32, 39]. In P. carotovorum SCC1, one type VI secretion system cluster is present in the genome (SCC1_0988–1002).
Soft rot pathogens have been suggested to be able to use insect vectors in transmission, and indeed, certain P. carotovorum strains can infect Drosophila flies and persist in their guts . This ability has been linked to the Evf ( Erwinia virulence factor) protein . The evf gene is present in the genome of P. carotovorum SCC1 suggesting that the strain may have the ability to interact with insects.
In this study, we presented the annotated genome sequence of the pectinolytic plant pathogen Pectobacterium carotovorum SCC1 consisting of a chromosome of 4,974,798 bp and a small cryptic plasmid of 5524 bp. Strain SCC1 was originally isolated from a diseased potato tuber and it has been used as a model strain to study interactions between soft rot pathogens and their host plants for decades. In accordance with the pathogenic lifestyle, the genome of strain SCC1 was found to harbor a large arsenal of plant cell wall-degrading enzymes similar to other sequenced Pectobacterium genomes. In addition, an insect interaction gene, evf, is present in the genome of strain SCC1 suggesting the possibility of insects as vectors or alternative hosts for this strain. The genome sequence will drive further the use of P. carotovorum SCC1 as a model plant pathogen.
We acknowledge the support of the Academy of Finland (Center of Excellence program 2006–2011, grants 213,509 and 129,628 and grants 136,470, 120,821, and 128,566), Biocentrum Helsinki, Biocenter Finland, University of Helsinki, the Emil Aaltonen foundation, the Finnish Doctoral Program in Computational Sciences FICS, the Viikki Doctoral Program in Molecular Biosciences, and the Finnish Doctoral Program in Plant Science.
ETP and MPi initiated the study and provided the strain and background information. HH isolated the genomic DNA. PL, PA and LP designed sequencing strategy and performed genome sequencing and assembly. PK, LH and ON annotated the genome. ON manually corrected the functional annotation. MPa and MPi conducted the phylogenetic analysis. ON, MPa and MPi performed biological experiments. ON, VP, JN and MPi analysed the contents of the genome. ON wrote the manuscript. MPi, PL and MPa contributed to writing. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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