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Solanum phureja strain:DM1-3 516R44

ABSTRACT: Solanum phureja strain:DM1-3 516R44 Genome sequencing

PROVIDER: PRJNA42071 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9418962.fastq.gz	Fastqsanger.gz
	SRR9418963.fastq.gz	Fastqsanger.gz
	SRR9418964.fastq.gz	Fastqsanger.gz
	SRR9418965.fastq.gz	Fastqsanger.gz
	SRR9418966.fastq.gz	Fastqsanger.gz

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The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.

Project description:Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.

| S-EPMC3203163 | biostudies-literature

EST mining of yellow potato and gene expression profiling of its infection by P. infestans using SAGE - SOLEXA

Project description:The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. The discovery and characterization of the proteins mediating this host–pathogen interaction enable the understanding of the pathosystem and is the key for developing resistant plants. Keywords: SAGE-Solexa, inoculation response, transcript profiling, Solanum phureja, Phytophthora infestans Four-week-old yellow potato (Solanum phureja) plants were inoculated with Phytophthora infestans and were collected and flash frozen in liquid nitrogen at 12 and 72 hours post inoculation, as well as mock inoculated, for RNA extraction. 2 yellow potato cultivars (resistant and susceptible) were used for each experiment. Mock inoculated plants were collected in each replicate. RNA obtained from each of the three biological replicates was pooled to obtain a single RNA sample for each timepoint X cultivar combination. A total of 6 different SAGE libraries were thus obtained. For all libraries, Illumina sequencing was performed at Canada´s Michael Smith Genome Sciences Centre.

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EST mining of yellow potato and gene expression profiling of its infection by P. infestans using SAGE - SOLEXA

2009-06-13 | GSE11781 | GEO

RNA sequencing of heart samples of myotonic dystrophic (DM1) patients

Project description:Analysis of alternative splicing in heart (left ventricles) samples of 3 adult DM1 patients versus 3 adult controls PolyA RNA from left ventricles (heart) of 3 controls and 3 DM1 patients were analysed by massive parrallel sequencing

2015-04-14 | E-GEOD-67812 | biostudies-arrayexpress

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