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 Create consensus sequence combining all BLAST matches on a particular contig/scaffold

Plant Genome Downloads http://phytozome.net

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

My Databases Citris clementina Citris sinensis Manihot esculenta Mimulus guttatus Ricinus communis Oryza sativa Carica papaya Fragaria vesca Zea mays Vitis choloroplast Arabidopsis chloroplast And Growing………..

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 MrBayes phylogenetic analysis

AGO4

Blasting Against Genome Database

Making Consensus

Concatenated Alignment

MUSCLE Alignment

Mr. Bayes Tree Builder Wow 13:18:22

AGO4 Tree Posterior

AGO4 Tree

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