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

Wow13:18:22

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