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![Page 1: 1 Development of tools for the analysis and visualisation of second generation sequencing data for Brassica species Chris Duran University of Queensland,](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649f1d5503460f94c3399f/html5/thumbnails/1.jpg)
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Development of tools for the analysis and visualisation of
second generation sequencing data for Brassica species
Chris DuranUniversity of Queensland, Australia
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Outline
• Brassica gene and promoter discovery: TAGdb• Brassica genome sequencing and annotation• Linking genetic and genomic data using CMap3D
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Paired-end short reads
Insert size
• Illumina GAIIx• Read length (35bp – 75bp)• Insert size up to 10Kbp
• ~ Normal distribution• Standard deviation ~ 10% mean
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Gene finding and extension
Gene/EST
Primer
genomic sequence
PCR
Known Unknown(Arabidopsis) (Brassica)
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TAGdb
http://flora.acpfg.com.au/tagdb/cgi-bin/results?jobID=bK85Lk10fVzMlw5e33FSuYBYr
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Example: AtWD40
![Page 8: 1 Development of tools for the analysis and visualisation of second generation sequencing data for Brassica species Chris Duran University of Queensland,](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649f1d5503460f94c3399f/html5/thumbnails/8.jpg)
Example: AtWD40
![Page 9: 1 Development of tools for the analysis and visualisation of second generation sequencing data for Brassica species Chris Duran University of Queensland,](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649f1d5503460f94c3399f/html5/thumbnails/9.jpg)
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Data
Brassica rapa 5 GbpBrassica oleracea 1 GbpBrassica nigra 1 GbpWheat 2.3 GbpWheat 7DS 4.2 GbpBarley 2.9 GbpPongamia 0.45 GbpNicotiana 10.2 Gbp
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TagDB
• Web-based tool for short read comparison• Short reads stored on server• User uploads query sequence
• http://flora.acpfg.com.au/tagdb
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Visualising read pairs for comparative genomics
genomic sequence
d
d
d
d
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B. rapa Chiifu
B. oleracea
B. nigra
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Genome annotation
500
1000
1500
1 10,000 30,000 50,000 70,000 90,000 107,001
Base pair (bp)
No.
of
alig
ned
read
s
0
High-covered regions of short reads and their corresponding annotation in a B. rapa BAC.
TIR-NBS-LRRαα α
MuDR Athila Athila solo LTR(AT)36
C/T-rich
region
Repeats
Predicted genic region
Genes
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CMap3D
• Finding the genes for the traits
• Integration of genetic data with genomic data• Mapping of QTL regions to genomic data
...
Annotation
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From genetic to physical maps
B. rapa scaffold
Ordered subset of SOAP2 output, with matching primer pairs highlighted
1448800 3546100
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Brassica CMap3D
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Brassica CMap3D
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Brassica CMap
• 23 map sets• 318 linkage groups• 4899 markers
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Summary
• There are a lot of useful things you can do with short paired read sequence data
• Use CMap3D to link Brassica genetics and genomics
• Tools available at: http://flora.acpfg.com.au/(or type ACPFG bioinformatics into Google)
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Acknowledgements
Paul Berkman
Lauren Bragg
Terry Clark
Dominic Eales
Chang Pyo Hong
Michael Imelfort
Edmund Ling
Megan McKenzie
Jiri Stiller
David Edwards
Daniel MarshallNikki ApplebyPing ZhangZoran Boskovic
Jacqueline Batley
Xiaowu Wang
Harsh Raman
Kaye Basford