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FMD Virus RT-PCR Control Samples

ABSTRACT: This study involved utilization of a DNA Plasmid that contained a full-length FMDV genome. The DNA plasmid was grown in bacteria before ultra-deep sequencing on a Illumina GAII. The Plasmid was then PCR amplified and again sequenced on a GAII, to asses the impact of PCR on the amount of observed mutations in the sequence data. The Plasmid was then transcribed, then reverse transcribed and PCR amplified before sequenced on a GAII, to asses the impact of RT on the amount of observed mutations in the sequence data. These control samples essentially allow the impact of sample processing on sequencing errors to be assessed in terms of viral quasispecies analyses.

PROVIDER: PRJEB8601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR776655.fastq.gz	Fastqsanger.gz
	ERR776656.fastq.gz	Fastqsanger.gz
	ERR776657.fastq.gz	Fastqsanger.gz
	ERR776658.fastq.gz	Fastqsanger.gz

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Iron acquisition system and cell shape of host bacteria commonly respond to the carriage of three plasmids belonging to different incompatibility groups.

Project description:Plasmids are one of the important mobile genetic elements in bacterial evolution. In this study, to evaluate the generality of the impact of plasmid carriage on host cell between different plasmids, we compared the response of Pseudomonas putida KT2440 to harboring three natural plasmids; RP4 (IncP-1, multidrug resistance, 60,099-bp), pCAR1 (IncP-7, carbazole-degradative, 200,231-bp) and NAH7 (IncP-9, naphthalene-degradative, 82,232-bp). We prepared two sets of plasmid-harboring strains from independent conjugation events to elucidate the reproducibility of the impact of the plasmid carriage. As results, the fitness was reduced by the carriage of RP4 and pCAR1 in liquid medium, while it was unaffected or even improved for NAH7-harboring strains. RP4-harboring KT2440 formed smaller colonies than the plasmid-free strain on solid medium (1.6% agar). The host cells were elongated by the carriage of the all plasmids, respectively. Copy number determination by quantitative PCR showed that the amount of each plasmid DNA in the host cell did not differed drastically. Whole genome resequencing showed that 13 SNPs (RP4), 24 SNPs (pCAR1) and 5 SNPs (NAH7) were the total differences between the two substrains for each plasmid-harboring strains. Transcriptome analyses showed that the impact of plasmid carriage was constantly larger in RP4-harboring strain than the other two plasmid-harboring strains. Genes involved in metal acquisition and metabolism were commonly affected by the carriage of the three plasmid. Indeed, plasmid-harboring strains showed greater growth inhibition than plasmid-free strains under iron-limiting condition. This feature could become future target to control plasmid spreading.

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