This document summarizes research analyzing plant resistance genes in saffron (Crocus sativus) using RNA-Seq data. The researchers collected saffron RNA-Seq data and plant resistance gene data. They mapped the data and annotated over 100,000 contigs assembled from over 26 million reads. BLAST analysis found hits for saffron resistance genes, with the highest numbers in stigma tissue. The genes were classified and RLPs, kinases, RLKs were most common. Further work proposed mapping the genes to a saffron genome when sequenced and clustering/classifying for polyploidy analysis.

1. 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, Iran
b Department of Biochemistry, University of Tehran, Tehran, Iran

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

4. Polyploidy form…………………………………….…………………………………..
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AutopolyploidyAllopolyploidy

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

6. Gene pattern of triploids
…CATGATCGATGTCGTAGCTACGAGTCACGTCTATATGCATCGAT…
…CATGATCCCTGTCGGAGCTACGAGTCCTGTCTATGATCATCGAT…
…CATGTTCGATGTCGGAGCTACGAGTCCTGTCTATATGCATCGAT…
…………………………………….…………………………………..
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You must see this pattern in multiple genes

7. Crocus Sativus (Saffron)…………………………………….…………………………………..
2N = 3X = 24
Genome = NOT Sequenced
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Parents
Economical importance

8. …………………………………….…………………………………..
Plant Resistance Genes
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9. STEP 1
Data collection
STEP 2
Data mapping
STEP 3
Annotation
STEP 4
Further Works
Project steps…………………………………….…………………………………..
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10. …………………………………….…………………………………..
Data collection
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Saffron RNA-Seq dataPlant resistance genes data

11. STEP 1
Data collection
STEP 2
Data mapping
STEP 3
Annotation
STEP 4
Further Works
Project steps…………………………………….…………………………………..
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12. Data mapping…………………………………….…………………………………..
Data
mapping
ASSEMBLY
GALAXYBLAST +
PYTHON BIOPYTHON
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13. STEP 1
Data collection
STEP 2
Data mapping
STEP 3
Annotation
STEP 4
Further Works
Project steps…………………………………….…………………………………..
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14. …………………………………….…………………………………..
Annotation
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Domain based
Sequence based

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

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

17. BLAST+ results…………………………………….…………………………………..
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18. Annotation results…………………………………….…………………………………..
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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

19. Annotation results…………………………………….…………………………………..
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Saffron PRG Classes
Total PRG contigs 753
Hits against PRGDB data
RLPs 282
Kinases 256
RLKs 144
CNL 63
TNL 57
Others 25

20. Conclusion
Extracellular, intracellular and Inter-membrane domains
Extracellular factors induced resistance
RLP, Kinase cooperation
Qualitative and quantitative resistance
Example: fungal chitin
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21. 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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22. …………………………………….…………………………………..
Further
work
MAPPING
GENOME
BROWSERS
MAPPING ON
GALAXY
CLUSTERING CLASSIFICATION
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23. Thank You
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