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Josh Stein Cold Spring Harbor Laboratory

Genome Database Comparative Genomics Phylogenomics Variation GrameneMart ( BioMart ) Discovery Environment. Josh Stein Cold Spring Harbor Laboratory. Exploring Plant Genomes. Browse Search Upload personal data Analysis tools. Gramene’s Key Strengths. Comparative genomics

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Josh Stein Cold Spring Harbor Laboratory

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  1. Genome DatabaseComparative GenomicsPhylogenomicsVariationGrameneMart (BioMart)Discovery Environment Josh Stein Cold Spring Harbor Laboratory

  2. Exploring Plant Genomes • Browse • Search • Upload personal data • Analysis tools

  3. Gramene’s Key Strengths • Comparative genomics • Complete reference genomes for 11 plant species including A. thaliana & A. lyrata • Whole genome alignments • Phylogenetic gene trees • Ability to upload and share data • Data mining using Gramene Mart • Extensive variation data sets for Arabidopsis • Integration with Pathways databases

  4. Quick entry points

  5. Browser tracks • Whole genome alignments • Synteny views • Location-based variation

  6. Gene sequence • Splice variants • Gene centered variation • Phylogenetic trees • Cross-reference to external databases

  7. Transcript & protein sequences • Protein structure • Transcript & protein based variation • GO and other ontologies

  8. Location View Browser Tracks TAIR 10 Annotation EST/cDNA alignments Array probes Repeats Variation Genome alignments -cross-species browsing

  9. Configuring Tracks

  10. Standard Analysis & Visualization • InterPro domain & GO functional annotation • Cross-reference to external ID’s • Whole Genome Alignment (Blastz-chain-net) • Phylogenetic Gene Trees (Compara) • Synteny Analysis • Consequences of SNP

  11. InterPro/dbXref/GO • Structural prediction: Pfam, PIRSF, PRINTS, PROSITE, SMART, SUPERFAMILY, TIGRFAM, TMHMM, SignalP • Cross-reference genes to 3rd party identifiers: Entrez Gene, PlantGDB, PUTs, RefSeq, Gene Index, UniGene, UniProtKb/Swissprot, NASC, IPI, WikiGene • Gene Ontology, Plant Ontology

  12. Alignment View • Pairwise BLASTZ-CHAIN-NET whole genome alignment • Arabidipsislyrata, Poplar, Grapevine • Rice, Brachypodium, Sorghum • Physcomitrella

  13. Multi-species View A. lyrata Arabidopsis Grapevine Arabidopsis Poplar

  14. Conserved non-coding regions

  15. View Sequence Alignment

  16. Phylogenetic Analysis Tools

  17. Compara Gene Trees Reconstructing evolutionary histories • Gene Trees for 11 plants plus human, Ciona, fly, worm, & yeast • Infers orthologs and paralogsby reconciling gene tree with input species tree • Taxonomic dating • ~35,000 trees • ~24,500 plant specific • ~10,000 containing Arabidopsis • 1059 specific to Arabidopsis genus • 79 specific to A. thaliana • 527 specific to A. lyrata http://useast.ensembl.org/info/docs/compara/homology_method.html Vilella A.J., et al. (2008). Genome Res. Pre-print:doi:10.1101/gr.073585.107

  18. Tree Viewer Speciation node = ortholog Duplication node = paralog

  19. NewickTree & Alignment (((ENSCINP00000002474_Cint_:0.0000, R10D12.12_Cele_:3.4477):0.7716, FBpp0084782_Dmel_:0.8566):0.0000, (((((BRADI3G43170.1_Bdis_:0.0615, BRADI2G38000.1_Bdis_:0.1536):0.0214, ((LOC_Os02g26814.1_Osat_:0.0000, BGIOSGA008178-PA_Oind_:0.0000):0.0000, ORGLA02G0140900.1_Ogla_:0.0000):0.0938):0.0231, (((GRMZM2G050705_P02_Zmay_:0.0099, GRMZM2G124671_P01_Zmay_:0.0745):0.0043, Sb08g016480.1_Sbic_:0.0348):0.0000, (GRMZM2G022470_P01_Zmay_:0.0475, Sb04g017490.1_Sbic_:0.1037):0.0000):0.0917):0.1118, (((POPTR_0005s03870.1_Ptri_:0.0420, POPTR_0013s02650.1_Ptri_:0.0427):0.0918, (GSVIVT01006266001_Vvin_:0.0342, GSVIVT01000019001_Vvin_:0.0817):0.1210):0.0363, ((scaffold_702792.1_Alyr_:0.0043, scaffold_603852.1_Alyr_:0.0632):0.0277, AT4G16710.1_Atha_:0.0204):0.2813):0.1261):0.5081, E_GW1.232.43.1_Ppat_:0.3698):0.3605):0.0000; ORGLA02G0140900.1_Ogla_ VFVTVGTTCF DALVKAVDSP QVKEALLEKG YTDLIIQMGR GTY------- BRADI2G38000.1_Bdis_ VFVTVGTTCF DALVKAVDSE EVKQALLRKG YTDLLIQMGR GTY------- GRMZM2G050705_P02_Zmay_ VFVTVGTTCF DALVMAVDSP EVKKALLQKG YSNLLIQMGR GTY------- POPTR_0005s03870.1_Ptri_ VFVTVGTTLF DALVRTVDTK EVKQELLRNG YTHLIIQMGR GSY------- GRMZM2G022470_P01_Zmay_ VFVTVGTTCF DALVMAVDSP EVKKTLLQKG YSNLLIQMGR GTY------- BRADI3G43170.1_Bdis_ VFVTVGTTCF DALVKKVDSP QVKEALWQKG YTDLFIQMGR GTY------- GSVIVT01006266001_Vvin_ VFVTVGTTCF DALVKAVDTQ EFKKELSARG YTHLLIQMGR GSY------- Sb08g016480.1_Sbic_ ---------- ----MAVDSP EVKMALLQKG YSNLLIQMGR GTY------- GRMZM2G124671_P01_Zmay_ VFVTVGTTCF DALVMAVDSP EVKKALLQKG YSNLLIQMGR GTY------- Sb04g017490.1_Sbic_ ---------- ----MAVASP EVKKALLQKG YSNLVIQMGR GTY------- BGIOSGA008178-PA_Oind_ ---------- ---------- ---------- ---------- ---------- E_GW1.232.43.1_Ppat_ VLVTVGTTLF DALVREASSQ PCRQVLADFG YSSLVIQRGK GSF------- scaffold_702792.1_Alyr_ VFVTVGTTSF DALVKAVVSE DVKDELQKRG FTHLLIQMGR GIF------- R10D12.12_Cele_ ---------- ---------- ---------- ---------- ---NQDVIDR ENSCINP00000002474_Cint_ IFVTVGTTSF DELTETITSK PVQKVLQSQG YDKVTIQYGR GKH------- scaffold_603852.1_Alyr_ VFVTVGTTSF DALVKAVVSE DVKDELQKRG FTHLLIQMGR GNF------- AT4G16710.1_Atha_ VFVTVGTTSF DALVKAVVSQ NVKDELQKRG FTHLLIQMGR GIF------- LOC_Os02g26814.1_Osat_ VFVTVGTTCF DALVKAVDSP QVKEALLEKG YTDLIIQMGR GTY------- GSVIVT01000019001_Vvin_ VFVTVGTTCF DALVKAVDTH EFKRELFARG YTHLLIQMGR GSY------- FBpp0084782_Dmel_ VYITVGTTKF DALISTASTE PALKALQNRK CTKLVIQHGN SQP------- POPTR_0013s02650.1_Ptri_ VFVTVGTTLF DALVRTVDTK EVKQELLRKG YTDLVIQMGR GSY-------

  20. Orthologs & Paralogs

  21. Gene-Centered Synteny Build Compara Orthologs Collinear mappings (DAGchainer) “in-range” mappings near collinear anchors Map

  22. Synteny View • Available for A. lyrata, grapevine, & poplar • Navigate to other genome • Ortholog browser • Link to multi-species view

  23. Browse across duplicated regions from polyploidy Chr 1 vs Poplar Chr 1 vs Grapevine Switch reference to grape

  24. Some Applications …

  25. Distinguish “Real” Genes From Transposons Domesticated TE • FAR1/FHY3 transcription factor family functions in light sensing • Evolved from Mu-related transposes • Cannot distinguish by BLAST FHY3 Missing annotation in A. lyrata? “Rule-in” functioning genes

  26. Enrich Annotations in Other Species Putative mis-annotated Grape gene • Arabidopsis and Rice orthologs both show one gene • Arabidopsis ortholog in correct syntenic context

  27. Adding Custom Tracks

  28. Custom Tracks • Methylome (Ecker) • Uploaded from an URL • BED file format • Salk T-DNA lines • Uploaded from my laptop • GFF file format • EST alignments from non-model plants • DAS: Distributed Annotation system • Protocol for sharing 3rd party data • DAS Registry

  29. Upload Your Data chr1 SALK T-DNA 1066 1097 7e-07 - . ID=SALK_082138.17.20.x chr1 SALK T-DNA 1066 1097 6e-07 + . ID=SALK_114475.16.50.x chr1 SALK T-DNA 1067 1093 3e-06 - . ID=SALK_065399.25.40.x chr1 SALK T-DNA 1073 1097 6e-05 - . ID=SALK_117416.15.55.n chr1 SALK T-DNA 1075 1099 6e-05 - . ID=SALK_132061.15.90.x chr1 SALK T-DNA 1076 1100 6e-05 - . ID=SALK_117013.15.75.n chr1 SALK T-DNA 1676 2070 0.0 - . ID=SALK_047276.52.80.x

  30. Attach From Remote File track name="mCIP col/met1 BU" color=darkgreen description="Methylation" useScore=3 visibility=2 height=30 chr1 25 49 mCIP_col/met1_BU 13.4997 chr1 60 84 mCIP_col/met1_BU 7.54671 chr1 113 137 mCIP_col/met1_BU 0.0145213 chr1 154 178 mCIP_col/met1_BU 0.15643 chr1 185 209 mCIP_col/met1_BU 0.000386254 chr1 219 243 mCIP_col/met1_BU 0.000218226

  31. Add DAS: Distributed Annotation System Protocol for sharing 3rd party data via a DAS registry • www.dasregistry.org • www.gramene.org/gramenedas/das/sources

  32. Manage Custom Tracks

  33. Turn On/Off Custom Tracks

  34. GrameneMart • Custom queries for bulk downloads • Powerful tool for data mining Orthologs in lyrata, grape, poplar, rice, Brachypodium, sorghum maize, & moss

  35. BioMart Use Cases All transmembrane-targeted genes, showing InterPro domains, GO terms, and AFFY id’s

  36. BioMart Use Case Evolution of cyclin genes: Taxon of origin for paralog pairs of cyclin-domain genes that have an ortholog in Physcomitrella

  37. BioMart Use Cases Mine germplasm for loss of function alleles in diversity populations: All Myb-domain genes with “STOP_GAINED” SNP allele

  38. Additional Data Access FTP: Data files, SQL dump, Software Read-only Public MySQL Web Services

  39. HELP!

  40. Contact Us

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