receptor-like proteins (rlps) and kinases are major classes of resistance genes in saffron (crocus...

In the name of Allah

Receptor-like proteins (RLPs) and kinases are major classes of resistance

genes in saffron (crocus sativus)

Ehsan Sepahia*, Ali Mohammad Banaei-Moghaddamb, Kaveh Kavousia

a Department of Bioinformatics, University of Tehran, Tehran, Iranb Department of Biochemistry, University of Tehran, Tehran, Iran

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The main questionIs it possible to address ploidy level and polyploidy form of an organism using RNA-Seq data?

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Ploidy level…………………………………….…………………………………..

Polyploid >>

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Polyploidy form…………………………………….…………………………………..

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The main question…………………………………….…………………………………..Is it possible to address ploidy level and polyploidy form of an organism using RNA-Seq data?

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Gene pattern of triploids

…CATGATCGATGTCGTAGCTACGAGTCACGTCTATATGCATCGAT…

…CATGATCCCTGTCGGAGCTACGAGTCCTGTCTATGATCATCGAT…

…CATGTTCGATGTCGGAGCTACGAGTCCTGTCTATATGCATCGAT…

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You must see this pattern in multiple genes

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Crocus Sativus (Saffron)…………………………………….…………………………………..

2N = 3X = 24Genome = NOT Sequenced

Parents

Economical importance

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…………………………………….…………………………………..Plant Resistance Genes

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STEP 1

Data collection

STEP 2

Data mapping

STEP 3

Annotation

STEP 4

Further Works

Project steps…………………………………….…………………………………..

…………………………………….…………………………………..Data collection

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Saffron RNA-Seq dataPlant resistance genes data

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STEP 1

Data collection

STEP 2

Data mapping

STEP 3

Annotation

STEP 4

Further Works

Project steps…………………………………….…………………………………..

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Data mapping…………………………………….…………………………………..

Data mapping

ASSEMBLY

GALAXYBLAST +

PYTHON BIOPYTHON

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STEP 1

Data collection

STEP 2

Data mapping

STEP 3

Annotation

STEP 4

Further Works

Project steps…………………………………….…………………………………..

…………………………………….…………………………………..Annotation

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Domain basedSequence based

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Assembly results…………………………………….…………………………………..

Assembly results for each of 6 data-sets

Total reads (each file) Over 26000000

Read length 90

Total contigs Over 100000

Contig N50 Over 1250

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BLAST+ results…………………………………….…………………………………..

tBLASTn results for 6 data-sets

Total PRGDB proteins 112

Hits against PRGDB data

Stigma data-set 1311

Stamen data-set 1109

Tepal data-set 854

Leaf data-set 1259

Corm data-set 973

ABRII data-set 1025

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BLAST+ results…………………………………….…………………………………..

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Annotation results…………………………………….…………………………………..

Total PRG contigs

Stigma data-set 712

Stamen data-set 658

Tepal data-set 577

Leaf data-set 689

Corm data-set 611

ABRII data-set 611

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Annotation results…………………………………….…………………………………..

Saffron PRG Classes

Total PRG contigs 753

Hits against PRGDB data

RLPs 282

Kinases 256

RLKs 144

CNL 63

TNL 57

Others 25

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ConclusionExtracellular, intracellular and Inter-membrane domainsExtracellular factors induced resistanceRLP, Kinase cooperationQualitative and quantitative resistanceExample: fungal chitin

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STEP 1

Data collection

STEP 2

Data mapping

STEP 3

Annotation

STEP 4

Further Works

The main questionIs it possible to address ploidy level and polyploidy form of an organism using RNA-Seq data?…………………………………….…………………………………..

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…………………………………….…………………………………..

Further work

MAPPING

GENOME BROWSE

RS

MAPPING ON

GALAXY

CLUSTERING

CLASSIFICATION

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Thank You