1 / 41

Exploring Plant Genomes through Gramene: Comparative Genomics and Phylogenomics Tools

Gramene offers an extensive platform for exploring plant genomes through comparative genomics and phylogenomics. This resource features complete reference genomes for 11 plant species, including Arabidopsis thaliana and A. lyrata. Users can perform whole genome alignments, analyze phylogenetic gene trees, and upload personal data for sharing and data mining using Gramene Mart. With additional tools for analyzing variation data, integrations with pathway databases, and opportunities for constructing gene trees, Gramene facilitates comprehensive research on plant evolutionary biology.

presley
Télécharger la présentation

Exploring Plant Genomes through Gramene: Comparative Genomics and Phylogenomics Tools

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related