Mining the Arabidopsis genome with the Arabidopsis Genome Resource

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Mining the Arabidopsis genome with the
Arabidopsis Genome Resource

• Keith Bradnam
• Nottingham Arabidopsis
• Stock Centre

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Some acronyms

• Arabidopsis Genome Resource
• AGR
• Nottingham Arabidopsis Stock Centre
• NASC
• UK Crop Plant Bioinformatics Network
• UK Cropnet
• GARNET
• Genomics Arabidopsis Resource Network

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Relationships
AGR
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Arabidopsis model organism

• Easy to grow
• Produces lots of seed
• Seed to seed in 8 weeks
• Completely mapped
• Closely related to other commercially important
  plants

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Arabidopsis the genome

• 130 Mb genome
• Five chromosomes
• Both major ecotypes have been sequenced
• First plant genome to be completed???

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Features of the genome

• Gaps will not be 100 sequenced
• Conserved blocks - synteny
• Many internal duplications
• Contain families of repeat sequences
• Many SNPs identified (1 per 3 kb)
• Compact, streamlined genome

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Smallest plant genome?
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About AGR

• A database based on the ACEDB database system
• Free to download and install locally
• Available for all computer platforms
• Web based access
• WebAce
• AceBrowser
• GFace

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What data is in AGR?

• Sequences (updated daily)
• AGI genome sequence (1,500 clones)
• EST and GSS sequences
• Organelle sequences
• Other ecotype sequences
• Protein sequences (Swissprot TREMBL)
• Insert sequences
• Over 200,000 sequences in total

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Other AGR data

• Maps and markers
• Physical, genetic, and recombinant inbred (RI)
  maps
• 1,200 RI markers
• RI scoring information
• Clone, Locus, and Allele info
• Germplasm info with links to order stocks

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Still more AGR data

• Bibliographic data (from EMBL records)
• Images (plants and gels)
• Other species info (protein sequences and
  associated info from all higher plant species)
• BLAST homologies millions of hits
• Mostly intra-specific homologies
• Some inter-specific homologies

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Accessing AGR

• On the web
• ukcrop.net
• ukcrop.net/agr/
• FTP sites
• ACEDB www.acedb.org
• AGR data
• ftp//nasc.nott.ac.uk/pub/uk-crop

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Xace screenshot 1
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UK Cropnet Screenshot 1
ukcrop.net/
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UK Cropnet Screenshot 2
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Acebrowser Screenshot 1
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Acebrowser Screenshot 2
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Acebrowser screenshot 3
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AGR page screenshot
ukcrop.net/agr/
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AGR page screenshot2
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Insert lines

• Many Arabidopsis plants now contain random
  transposon insertions
• Therefore genes of interest may be hit, or
  modified by inserts
• Genomic location of inserts identified by blast
  analysis
• Can only identify putative location

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Insert data in AGR

• SINS (Jones) inserts
• Stocks sequences
• IMA (Sundaresan) inserts
• Stocks some location info
• ITS (Pereira) inserts
• Just sequences
• Separate web page for inserts
• ukcrop.net/agr/insert.html

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Xace screenshot
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Webace screenshot
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Searching for inserts
Find sequence of interest in AGR
Look to see if sequence has homology to an insert
BLAST search your sequence against insert
sequences
Search against precomputed BLAST analysis
Look to see if corresponding stocks are available
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NASC blast server
nasc.nott.ac.uk/blast.html
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Search precomputed blast data
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Future developments

• More data
• Microarray data
• More insert sequences
• Improved access to data
• New look to Acebrowser interface
• Bring GFace interface online
• More links between NASC and AGR

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More developments

• Better organisation of data
• Sequence maps post genome
• More intuitive searching, e.g. gene name
• More links to other DBs?
• New server faster access

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Acknowledgements

• NASC
• Sean May
• Jamie Kincaid
• UK Cropnet