A tutorial introduction into the MIPS PlantsDB barley&wheat databases. Manuel Spannagl&Kai Bader transplant user training Poznan June 2013

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A tutorial introduction into the MIPS PlantsDB barley&wheat databases Manuel Spannagl&Kai Bader transplant user training Poznan June 2013

MIPS PlantsDB tutorial - some exercises Please go to: http://mips.helmholtz-muenchen.de/plant/genomes.jsp

Tutorial objectives Search and navigate the MIPS PlantsDB instances Understand triticeae data concepts&contents and access Search and navigate the triticeae GenomeZippers Learn how to use the CrowsNest Synteny browser Use BLAST to identify candidate genes Download batch files to your local machine for further analysis

Access to species databases

Exercise 1 Go to the MIPS PlantsDB home page at http://mips.helmholtzmuenchen.de/plant/genomes.jsp Find all information available in PlantsDB about the Barley gene MLOC_67600.1 On what contig is it located? How many Barley genes do you find searching for WUSCHEL-related homeobox?

Exercise 2 Find details about a gene in the MIPS PlantsDB barley DB Find all barley genes carrying the annotation Alpha-glucosidase and open the gene report of the fourth hit (MLOC_68876.3) Identify the putative orthologs in other plant species and putative paralogs in barley how many are there and for what organisms do you find some? (hint: use gene family information) Download the genes protein and CDS sequence

Exercise 3 - background Brachypodium distachyon is a model organism for related, but much more complex triticeae species such as wheat and barley.

Exercise 3 Query complex genomes using reference organisms the barley GenomeZipper Can you identify the (approximate) location of the barley locus orthologous/syntenic to the brachypodium gene Bradi2g39900.1 on the barley genome? What chromosome is it on, what is the appr. cm position? What marker is responsible for this anchoring? Are there any other genes in this syntenic position?

Exercise 4 - background Many related plant genomes share long stretches of conserved gene order: synteny This feature can be used to transfer knowledge from model to crop organisms Visualization of synteny is needed: CrowsNest tool Displays pre-calculated syntenic regions Browse from macro- to micro-synteny levels Integration of add. features such as Ka/Ks, gene families, density and heatmap plots

Exercise 4 - background http://mips.helmholtz-muenchen.de/plant/crowsnest/index.jsp

Exercise 4 Explore syntenic relationships between related plant genomes the CrowsNest tool Open the gene report of the Brachypodium gene from exercise 3: Bradi2g39900.1 Start CrowsNest by clicking CrowsNest_SyntenyToBarley and explore the syntenic relationship of this gene region with barley What barley region is syntenic to the Bradi2g39900.1 gene region, what chromosome and what gene? Is there an inversion on that chr.?

Exercise 5 Search for homologous genes in barley for your own sequence BLAST tool Download the DNA sequence from: ftp://ftpmips.helmholtzmuenchen.de/plants/user_training/unknowngrassseq.fa Use BLAST to identify the best matching barley (HC) gene model for this sequence: http://webblast.ipk-gatersleben.de/barley/viroblast.php Remember the found barley gene identifier and search for it in MIPS PlantsDB barley

Exercise 5 continued Search for homologous genes in barley for your own sequence BLAST tool What kind of function does the barley gene likely perform? What functional domains (PFAM, Interpro) are annotated for that gene?

Exercise 6 Query complex genomes using reference organisms extract wheat genic sequence Download the DNA sequence from: Use BLAST to identify the best matching representative grass gene model for this sequence: ftp://ftpmips.helmholtzmuenchen.de/plants/user_training/unknowngrassseq.fa http://mips.helmholtzmuenchen.de/plant/wheat/uk454survey/searchjsp/index.jsp Extract&download the wheat sub-assembly sequences for the identified rep. Grass gene

Exercise 6 continued Query complex genomes using reference organisms extract wheat genic sequence Open the downloaded file What kind of information do you find encoded in the gene fragment identifiers?

Exercise 7 Download bulk genome data from MIPS PlantsDB Download all the protein sequences annotated for the barley genome Is there any categorization for these genes (such as confidence classes)? What kind of additional data is available as bulk download for barley?

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