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Gene Prediction and Phylogenetic Trees

Gene Prediction and Phylogenetic Trees. Jared Mimms. Using Geneious and Internal Blast. Genbank deficient Make databases Illumina Contigs 454 Scaffolds ESTs Other plant genomes Search for genes using internal BLAST

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Gene Prediction and Phylogenetic Trees

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  1. Gene Prediction and Phylogenetic Trees Jared Mimms

  2. Using Geneious and Internal Blast • Genbank deficient • Make databases • IlluminaContigs • 454 Scaffolds • ESTs • Other plant genomes • Search for genes using internal BLAST • Create consensus sequence combining all BLAST matches on a particular contig/scaffold

  3. Plant Genome Downloads http://phytozome.net

  4. Other Downloadable Datasets http://www.plantgdb.org https://strawberry.plantandfood.co.nz/gbrowse/navbar/strawberry/download.html

  5. My Databases • Citrisclementina • Citrissinensis • Manihotesculenta • Mimulusguttatus • Ricinuscommunis • Oryza sativa • Carica papaya • Fragariavesca • Zeamays • Vitischoloroplast • Arabidopsis chloroplast • And Growing………..

  6. Example: AGO4 • BLASTn Arabidopsis vs. Genome Databases • Select all hits from same contig/scaffold/BAC/chromosome • Concatenate hits relative to Arabidopsis AGO4 gene (coding and noncoding segments) • Isolate predicted gene • Repeat for many species • Run MUSCLE alignment • Run MrBayesphylogenetic analysis

  7. AGO4

  8. Blasting Against Genome Database

  9. Making Consensus

  10. Concatenated Alignment

  11. MUSCLE Alignment

  12. Mr. Bayes Tree Builder Wow 13:18:22

  13. AGO4 Tree Posterior

  14. AGO4 Tree

  15. Future Directions • It’s go time baby… • ramp up to methytransferases • Standardize annotation formats (.xml) • CG analysis, role in CpG, CpNpG methylation • Promoter anlayses • Trees for entire genome • Get scaffolders up and running (Bambus) (need paired end?) Expand database to all publically available organism sequencing data (download all ftp’s) Internal Cloud

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