Dataset Information

Draft genome sequencing data of a pathogenic Pantoea stewartii subspecies stewartii strain SQT1 causing bronzing disease of jackfruit in Malaysia.

ABSTRACT: A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 bp with a G+C content of 53.7%. A total protein of 4,671 was identified including virulence factors, resistance factors and secretion systems. Pantoea stewartii subsp. stewartii strain DC283 (NCBI accession no. CP017581.1) was used as a reference genome, where the query hit 72% coverage and average sequencing depth of 68. In total, 28,717 nucleotide polymorphisms, 520 small insertion/deletions and 142 structure variants were identified. The complete genome was deposited at the European Nucleotide Archive under the sample accession number ERP119356 and study accession number PRJEB36196.

SUBMITTER: Ibrahim R

PROVIDER: S-EPMC7205738 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Draft genome sequencing data of a pathogenic Pantoea stewartii subspecies stewartii strain SQT1 causing bronzing disease of jackfruit in Malaysia.

Ibrahim Rohaya R Ismail-Suhaimy Noor Wahida NW Shu-Qing Tan T Ismail Siti Izera SI Ina-Salwany Md Yasin MY Yusof Mohd Termizi MT Hakiman Mansor M Karam Daljit Singh DS Zulperi Dzarifah D

Data in brief 20200430

A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 b ...[more]

PMID: 32395592

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Project description:Following a request from the European Commission, the EFSA Panel on Plant Health performed a risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA. This pest is a Gram-negative bacterium which causes Stewart's vascular wilt and leaf blight of maize (including sweet corn), a disease responsible for serious crop losses throughout the world. The following scenarios were considered: scenario A0 (current practice), scenario A1 (US request for modification of EU conditions for derogation), and scenario A2 (EU conditions for derogation). Results from the quantitative seed pathway model presented here show that, despite the low rates of plant-to-seed and seed-to-seedling transmission that have been reported in the literature for Stewart's wilt, given the amount of traded seed, and in the case of voluntary (i.e. not mandatory) inspections of seed production fields at the origin (i.e. scenario A0), the frequency of introducing the disease is in the order of magnitude of some hundred introductions per year (median number). The EU conditions for derogation would lead to a decrease in the likelihood of entry compared to scenarios A0 (about 10,000 times fewer introductions) and A1 (about 2,000 times fewer introductions). This protective effect is mainly due to the requirement that only genotypes resistant to Stewart's wilt are traded, with the additional field inspection (two instead of one per season) providing additional reassurance. The Panel also concluded that seed lot inspections, as currently carried out (e.g. with a sample of 400 seeds) are not likely to lead to a relevant reduction in the level of infected imported maize seed, given the low prevalence of Stewart's wilt at the origin. If, however, there is aggregation in infection among consignments, inspection would work towards identifying the highly infected consignments. Recently, outbreaks of Stewart's wilt have occurred in Italy (Emilia Romagna, Friuli, Lombardy and Veneto). A review is provided of the available information to assess the possible role of seed imports in these outbreaks.

Dataset Information

Draft genome sequencing data of a pathogenic Pantoea stewartii subspecies stewartii strain SQT1 causing bronzing disease of jackfruit in Malaysia.

Publications

Draft genome sequencing data of a pathogenic <i>Pantoea stewartii</i> subspecies <i>stewartii</i> strain SQT1 causing bronzing disease of jackfruit in Malaysia.

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