Abstract
Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of Pantoea sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.
GENOME ANNOUNCEMENT
Pantoea spp. are members of the family Enterobacteriaceae that have traditionally been regarded as saprophytes with a cosmopolitan distribution. Recent taxonomic studies have separated the genus into groups of biocontrol, plant, and clinical strains (10, 11). Previously, we demonstrated that Pantoea sp. strain Sc 1 is a causal agent of an emerging disease of immature green cotton bolls in southeastern Cotton Belt states and is vectored by boll-piercing insects such as stink bugs (6, 8, 9).
The draft genome sequence (50-fold coverage) of strain Sc 1 was generated using a Roche 454 GS-Junior DNA analyzer (454 Life Sciences, Branford, CT). A GS Titanium shotgun library (Roche) was prepared, and two runs were pyrosequenced, yielding 76 Mb (187,123 reads with an average length of 410 bases) and 57 Mb (129,858 reads with an average length of 445 bases). Using the same genomic DNA stock, 3- and 8-kb paired-end Titanium libraries were constructed and pyrosequenced, producing 30 Mb (96,198 reads with 70,100 paired reads) and 51 Mb (173,866 reads with 118,148 paired reads), respectively. The genome was constructed using GS De Novo Assembler 454 (Life Sciences, Branford, CT), resulting in four scaffolds totaling 4.4 Mb. Only the largest scaffold (3.8 Mb) contained contig gaps that were closed by cloning and sequencing (BigDye Chemistry) PCR products and employing an ABI PRISM 3100 genetic analyzer (Applied Biosystems, Carlsbad, CA).
Putative coding sequences were predicted by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP), which uses a combination of GLIMMER (2, 3), GeneMark (1), and tRNAScan-SE (7) and searches several protein databases (Entrez Protein Clusters, Conserved Domain Databases, and Clusters of Orthologous Groups). The PGAAP results were then manually curated. Manual annotation was also conducted using the NCBI BLAST program.
The G-C content was 57%, and extrachromosomal DNA was not detected. The genome contained a total of 4,061 predicted coding sequences (CDS), 5 rRNA operons, and 67 tRNAs. Predicted open reading frames (ORFs) showed considerable homology with components of both type IV and VI secretion systems that are reportedly involved in plant pathogenesis (4, 5) and may be involved in cotton disease. Sequencing the genome of strain Sc 1 is an important step in identifying putative genes involved in cotton boll infection.
Nucleotide sequence accession numbers.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AJFP00000000. The version described in this paper is the first version, AJFP00000000.1.
ACKNOWLEDGMENTS
Thanks are due to Cyndy Menn for technical assistance in sequencing, Shannon Ng for editing the manuscript, and Sandra Truong for providing key annotation support.
This work was supported by the USDA CRIS project number 6202-22000-026-00D.
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