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Study to define NLRomes in multiple Solanaceae accessions using R gene enrichment and sequencing in combination with PacBio SMRT sequencing

Identifiers: SRA: ERP104712
BioProject: PRJEB22982
JIC: ena-STUDY-JIC-11-10-2017-14:00:49:481-768
The John Innes Centre: ena-STUDY-JIC-11-10-2017-14:00:49:481-768
Study Type: 
Other
Abstract: To combat pathogens, plants evolved both cell surface and intracellular receptors. The intracellular receptors are usually encoded by disease resistance (R) genes, many of which have been exploited by breeders for centuries. R genes usually encode nucleotide binding, leucine-rich repeat proteins, referred to as NLR proteins, that enable the plant to activate its powerful defence mechanisms only upon detection of specific pathogen molecules. Most plant genomes carry many scores or hundreds of NLR genes, many of which form extensive allelic series. The aim of this project is to define NLRomes in multiple Solanaceae accessions using R gene enrichment and sequencing (RenSeq, Jupe et al, Plant J, 76: 530-544 (2013)) in combination with PacBio SMRT sequencing (SMRT RenSeq, Witek et al, Nat Biotech, 34:656-660 (2016)). To enrich samples for NLR sequences prior PacBio sequencing, targeted enrichment was performed for Nicotiana spp. using bait library published by Witek et al (Nat Biotech, 34:656-660 (2016)). Remaining Solanum spp. samples were enriched with the bait library containing 60k RNA oligos targeting NLRs from various Solanum spp (Witek et al, in preparation).
Description: To combat pathogens, plants evolved both cell surface and intracellular receptors. The intracellular receptors are usually encoded by disease resistance (R) genes, many of which have been exploited by breeders for centuries. R genes usually encode nucleotide binding, leucine-rich repeat proteins, referred to as NLR proteins, that enable the plant to activate its powerful defence mechanisms only upon detection of specific pathogen molecules. Most plant genomes carry many scores or hundreds of NLR genes, many of which form extensive allelic series. The aim of this project is to define NLRomes in multiple Solanaceae accessions using R gene enrichment and sequencing (RenSeq, Jupe et al, Plant J, 76: 530-544 (2013)) in combination with PacBio SMRT sequencing (SMRT RenSeq, Witek et al, Nat Biotech, 34:656-660 (2016)). To enrich samples for NLR sequences prior PacBio sequencing, targeted enrichment was performed for Nicotiana spp. using bait library published by Witek et al (Nat Biotech, 34:656-660 (2016)). Remaining Solanum spp. samples were enriched with the bait library containing 60k RNA oligos targeting NLRs from various Solanum spp (Witek et al, in preparation).

Related SRA data

Experiments:
8 ( 8 samples )
Runs:
8 (21.1Gbp; 6.4Gb)
Additional objects:
File type count
pacbio_native 8