Genome Sequence of Pectobacterium sp. Strain SCC3193

Abstract

We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium Pectobacterium sp. strain SCC3193, a model strain isolated from potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp chromosome, with no plasmids.

GENOME ANNOUNCEMENT

Members of the genus Pectobacterium cause soft rot and blackleg disease in a wide range of plants, including economically important crop species such as potato (1). Pectobacterium sp. strain SCC3193 has been a model strain in the research of soft rot molecular biology for over 2 decades. It was isolated from potato stem on a Finnish field in the 1980s (8). SCC3193 was originally characterized as Pectobacterium carotovorum but the species status is, at this point, unclear. Previously sequenced Pectobacterium species are P. atrosepticum strain SCRI1043, P. carotovorum strain WPP14, P. brasiliensis strain PBR1692, P. carotovorum subsp. carotovorum strain PC1, and P. wasabiae strain WPP163.

The genome was sequenced using a hybrid approach combining data from three different technologies. First, a fragment library was produced and sequenced with the 454 Genome Sequencer GS20 (6), yielding 712,702 reads, with a mean read length of 101 bp and a total of 71,982,902 bp (ca. 14× coverage). A fosmid library was constructed by shearing genomic DNA cloned in the CopyControl pCC1FOS vector (Epicentre, Madison, WI) mechanically with a needle. End sequences were determined from 865 fosmids using BigDye chemistry and analyzed on ABI 3730 (Applied Biosystems, Foster City, CA), yielding a total of 1,047,795 bp. In addition, we constructed a fragment library for sequencing using SOLiD 2 chemistry (Applied Biosystems, Foster City, CA), with a read length of 35 bp. A total of 52,618,885 reads were obtained, of which 26,309,443 were mapped to the assembly (920,830,488 bp), giving a coverage of 184.

The assembly of 454 reads was performed using Newbler (Roche) and fosmid end sequences were used for the scaffolding of the obtained contigs. The genome was closed using PCR or linker PCR on genomic DNA or fosmids and direct sequencing of the obtained products. Homopolymer errors obtained by 454 sequencing and assembly were corrected by mapping the SOLiD reads to closed genome sequence. The editing and closing of gaps were done in Gap4 from the Staden Package (9).

Coding sequences (CDSs) were predicted using the Prodigal gene prediction program (2). GenePRIMP (7) was run to correct systematic errors made by Prodigal and to reanalyze the remaining intergenic regions for missed CDSs. Functional annotation was performed by using the PANNZER annotation tool (J. P. Koskinen, P. Törönen, J. Nokso-Koivisto, and L. Holm, unpublished data). The tRNA and rRNA genes were annotated using the tRNAscan-SE 1.23 (5) and RNAmmer 1.2 software programs (3). Orthologous groups between the different closely related proteomes were identified using OrthoMCL (4).

The genome of Pectobacterium sp. SCC3193 consists of a single circular chromosome that is 5.16 Mbp in size, with an overall G+C content of 50%, without any plasmids. The chromosomal genome contains 4,705 predicted protein-coding sequences, 76 tRNA genes, 7 rRNA operons, and 2 CRISPR loci. Based on the orthologous grouping, 772 (16%) of the SCC3193 CDSs have no detectable homologs in any of the complete Pectobacterium or Dickeya proteomes published to date.

Nucleotide sequence accession number.

The genome sequence of Pectobacterium sp. SCC3193 was deposited in GenBank under the accession number CP003415.