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Whole genome sequencing of Chlamydia isolates from birds

ABSTRACT: Illumina Miseq genome sequencing of Chlamydia isolates from birds

PROVIDER: PRJEB25740 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR2593863_1.fastq.gz	Fastqsanger.gz
	ERR2593863_2.fastq.gz	Fastqsanger.gz

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Project description:We present highly replicated whole transcriptome gene expression profiles of schizont-stage malaria parasites using RNA-seq analysis of multiple clinical isolates and laboratory-adapted lines Methods: Transcript profiles of schizont-stage laboratory-adapted and clinical malaria parasite isolates were generated by RNA sequencing. Five to ten replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Paired-end fastQ files were aligned using hisat2 and converted to indexed bam files using samtools. Bam files were filtered to exclude reads with MAPQ scores below 60. Reads were counted using SummarizeOverlaps feature of the GenomicAlignments package in R. Differential expression analysis was conducted using DESeq2 in R. qRT–PCR validation of differentially expressed genes was performed using SYBR Green assays for eight genes. Results: We show that increasing sample replication improves the true-positive discovery rate, and that when fewer replicates are available, focussing on the most highly expressed genes maintains the true-positive discovery rate. We identify schizont-stage genes that appear to alter in expression through the process of culture adaptation, as well as genes that show variable expression between isolates. We extend transcript quantitation for variably expressed genes to an even wider panel of ex vivo clinical isolate samples. Conclusions: Our study represents the first detailed analysis of replicated P. falciparum schizont-stage transcriptomes. Our data show that high levels of replication are necessary to capture gene expression differences among parasite isolates. We identify schizont-stage expressed genes that may be differentially expressed as a mechanism of immune evasion.

2018-04-27 | GSE113718 | GEO

ESGI Whole Genome Sequencing of samples from the Cilentogen isolates

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Whole-Genome Sequences of Eight Campylobacter jejuni Isolates from Wild Birds.

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Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan.

Project description:BACKGROUND:Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. METHODS:This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. RESULTS:All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). CONCLUSIONS:Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.

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