Post on 16-Jan-2017
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