SGN UPLB 2016
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The Sol Genomics Network provides bioinformatics tools for plant genomics and breeding research. It hosts genome sequences and data for several crops including tomato, potato, tobacco, pepper, and coffee. Tools on the site include JBrowse for genome browsing, BLAST for sequence searches, and tools for managing breeding programs. The network also develops specialized tools like one for designing virus-induced gene silencing constructs and a high-resolution tomato gene expression atlas. The presentation highlighted these genomics resources and tools to support research on solanaceous and other crops.
SGN UPLB 2016
- 1. Sol Genomics Network The Sol Genomics Network bioinformatics tools for genomics and breeding UPLB January, 2016 Noe Fernandez-Pozo
- 2. Ithaca
- 4. Sol Genomics Network https://solgenomics.net Sol Genomics Network
- 5. Sol Genomics Network Solanum Genomes Solanum tuberosum Solanum melongena Solanum pennellii Solanum lycopersicum Solanum pimpinellifolium Draft Genome Draft Genome
- 6. Sol Genomics Network Nicotiana Genomes Nicotiana sylvestris & Nicotiana tomentosiformis Draft Genome Nicotiana benthamiana Draft Genome Nicotiana tabacum Draft Genome N. tabacum K326 (Flue-cured) N. tabacum TN90 (Burley) N. tabacum Basma Xanthi (BX, Oriental)
- 7. Sol Genomics Network Other Genomes Capsicum annuum Capsicum annuum Zunla-1 Capsicum annuum var. glabriusculum Capsicum annuum cv. CM334 Capsicum chinense Coffea canephora Petunia spp. Coming soon …
- 8. Sol Genomics Network New responsive design
- 9. Sol Genomics Network The SGN carousel linked to the genome paper Direct access to JBrowse, BLAST, and the genome data More visibility for news, events and biological data
- 10. Sol Genomics Network The SGN carousel
- 11. Sol Genomics Network The SGN carousel
- 12. Sol Genomics Network Locus editors
- 13. https://solgenomics.net SGN Sol Genomics Network https://github.com/solgenomics https://citrusgreening.org CitrusGreening https://cassavabase.org CassavaBase https://yambase.org YamBase https://sweetpotatobase.org SweetPotatoBase https://musabase.org MusaBase
- 14. Sol Genomics Network Breeding Informatics CassavaBase Genotyping Data (GBS) Breeding Decisions Phenotyping Data Android FieldBook
- 15. Sol Genomics Network Cassava Crop • Tropical and subtropical regions • Mainly grown for starchy roots • Native to South America • Major crop in Africa • Food for 500 million people around the world • Clonally propagated • Accumulates toxic cyanogenic glucosides • Requires processing before consumption
- 16. Sol Genomics Network CassavaBase Data • 80,000 accessions • 1,500 trials • 7,800,000 phenotypic observations • ~12,000 genotypes • ~2,000,000,000 marker scores
- 22. Sol Genomics Network Genomic Selection
- 23. Sol Genomics Network Genomic Selection Tool Phenotypic values! Population Structure! GEBV vs phenotypes!
- 24. Sol Genomics Network Genomic Selection Tool Phenotypic values! Population Structure! GEBV vs phenotypes!
- 25. Sol Genomics Network GMOD Tools The Generic Model Organism Database project, a collection of open source software tools for managing, visualizing, storing, and disseminating genetic and genomic data.
- 30. Sol Genomics Network gene models, markers, SNPs, RNA-Seq data …
- 31. Sol Genomics Network gene models, markers, SNPs, RNA-Seq data … Tomato genes linked to SGN on click Right click view details, highlight, zoom
- 32. Sol Genomics Network gene models, markers, SNPs, RNA-Seq data …
- 33. Sol Genomics Network gene models, markers, SNPs, RNA-Seq data … save data for region or whole track, GFF3, BED, Fasta
- 34. Sol Genomics Network 360 Tomato variants
- 35. Sol Genomics Network 360 Tomato variants
- 36. Sol Genomics Network JBrowse: Nicotiana benthamiana bam files alignments and coverage Nicotiana benthamiana
- 47. Sol Genomics Network Gregory Martin Hernan Rosli Lukas Mueller SGNVIGS Tools http://vigs.solgenomics.net
- 48. Sol Genomics Network Virus-Induced Gene Silencing (VIGS) transformation mediated by A.tumefaciens or virus Ti Figure adapted from Azorsa et al. 2006 digested mRNA Azorsa D. et al. Gene silencing through RNA interference. (2006). Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules. Editors: Janson C.G. and During M.J. pp 252-264 21-24 nt
- 49. Sol Genomics Network VIGS Tool input
- 50. Sol Genomics Network VIGS Tool output
- 51. Sol Genomics Network VIGS Tool output
- 52. Sol Genomics Network VIGS Tool output
- 53. Sol Genomics Network VIGS Tool output
- 54. Sol Genomics Network VIGS Tool output
- 55. Sol Genomics Network VIGS Tool output
- 56. Sol Genomics Network VIGS Tool output Target genes Off-Target genes Score Graph Predicted region Custom region
- 57. Sol Genomics Network 2 6 6 8 9 92 94 1315 2344 VIGS Tool Graph ExpandedView every siRNA mapped is shown
- 59. Sol Genomics Network VIGS Tool algorithm The SGNVIGS tool simulates in silico the recognition of the mRNA by RISC and the siRNA, and tries to predict the best construct avoiding off-targets Print results Change number of targets Change Fragment size Selected species gene database input gene for silencing fragment in n-mer size Bowtie mapping Parse Bowtie result Set number of targets Calculate scores Predict best construct Change n-mer size Change number of mismatches
- 60. Sol Genomics Network Jocelyn Rose Carmen Catala James Giovannoni Lukas Mueller Zhangjun Fei David Domozych Skidmore College William Willats University of Copenhagen Alisdair Fernie Max Planck Institute Collaborators Noe Fernandez Yi Zheng Philippe Nicolas Richard Pattison Laetitia Martin Stephen Snyder Yoshi Shinozaki Yimin Xu
- 61. Sol Genomics Network Tissue homogenization Organ/tissue homogenization: 1 Outer Epidermis 3-5 Collenchyma 1 Inner Epidermis 16-18 Parenchyma Vascular tissue - Loss of valuable spatial information: biochemical pathway and regulatory networks - Significant dilution effects
- 62. Sol Genomics Network Laser Capture Microdissection Small green fruit Outer Epidermis Parenchyma Vascular Tissue Inner Epidermis Collenchyma
- 63. Sol Genomics Network Computed Tomography images and videos
- 64. Sol Genomics Network Computed Tomography images and videos
- 66. Sol Genomics Network Tomato Expression Atlas Expression displayed on microscopy images Linked to SGN data
- 67. Sol Genomics Network Tomato Expression Atlas Expression displayed on microscopy images Linked to SGN data
- 68. Sol Genomics Network Tomato Expression Atlas Expression displayed on microscopy images Linked to SGN data
- 71. Sol Genomics Network Carmen Catala Many genes preferentially expressed in the funiculus are absent from whole fruit RNA-Seq data • Contributes small proportion to total fruit volume • High transport between seeds and the rest of the fruit
- 72. Sol Genomics Network Carmen Catala Many genes preferentially expressed in the funiculus are absent from whole fruit RNA-Seq data • Contributes small proportion to total fruit volume • High transport between seeds and the rest of the fruit pericarp placenta septum funiculus
- 73. Sol Genomics Network Xyloglucan endotransglucosylase-hydrolases Iben Sorensen
- 74. Sol Genomics Network stem equator style SIXTH3 Xyloglucan endotransglucosylase-hydrolases Iben Sorensen
- 75. Sol Genomics Network Conclusions funiculus Many tissues for a higher resolution vs Whole fruit stem equator style Several fruit sections Laser micro-dissected tissues for a higher resolution
- 76. Sol Genomics Network Summary • Breeders Tools to manage breeder programs • GMOD Tools common bioinformatics tools implemented on SGN • SGN VIGS Tool to design VIGS constructs • Tomato expression Atlas, a high resolution expression atlas for tomato fruit developmental stages
- 78. Thank you for your attention ! Sol Genomics Network