2013 iPlant workshop Marcela Karey Monaco

2013 What is Gramene? An integrated plant reference genome resource Comparative genomics hub of data & tools for the analysis and visualization of plant genomes data informed by evolutionary histories Genome sequence, gene annotations, genetic & structural variants, metabolic & regulatory pathways

2013 Gramene offers… Genome sequence & gene annotations – 28 complete & 9 partial reference genome assemblies

2013 Gramene Release complete reference genomes 15 Monocots 9 Eudicots 4 Lower plants 9 partial assemblies Fully sequenced reference genomes in Gramene

2013 Gramene offers… Genome sequence & gene annotations – 28 complete & 9 partial reference genome assemblies – Variation data for 9 plant varieties

2013 Variation in Gramene Ensembl Browsers SpeciesVariantsSourceStudies Oryza sativa ssp japonica3,332, K SNPs x 20 accessions 1311 SNPs x 395 accessions NCBI dbSNP McNally et al. (2009). PNAS 106: Zhao et al PLoS ONE. 5:e10780 Oryza sativa ssp indica4,747,883 NCBI dbSNP Zea mays50,719,843 HapMap1: NAM founder lines HapMap2: pre-domesticated & domesticated lines Gore et al Science 326: Chia et al Genet 44: Arabidopsis thaliana 14,234,197 SV: 13, K SNPs x 1179 accessions 1001 genomes project: 411 resequenced accessions Atwell et al Nature. 465: Brachypodium distachyon327,988 2 accessions of Brachypodium sylvaticum Fox et al. (2013) Applications in Plant Sciences 1(3): Vitis vinifera457,404 Resequencing USDA germplasm collection Myles S, et al PLoS ONE. 5:e8219. Hordeum vulgare12,994,003 Resequencing 4 accessions plus wild barely The International Barley Genome Sequencing Consortium Nature 491, 711–716 Oryza glaberrima7,704,409 Resequenced 20 accessions African rice & wild progenitor Oryza Genome Evolution project Sorghum bicolorSV: 64,507 Structural variants from Database of Genomic Variants archive (dGVA) Zheng et al Genome Biol.. 12:R114.

2013 Gramene offers… Genome sequence & gene annotations – 28 complete & 9 partial reference genome assemblies – Variation data for 9 plant varieties Comparative analysis – Phylogenetic gene trees => Ortholog predictions – 56 whole genome alignments – 20 synteny maps

2013 Gramene offers… Genome sequence & gene annotations Comparative analysis New functionalities – Highlight gene trees with InterPro & GO – Variant Effect Predictor service: user loads VCF – Upload private data and view in browser (BAM, VCF, GFF) – Assembly converter service

2013 Demo of

2013 Gramene offers… Genome sequence & gene annotations Comparative analysis Tools & services – Genome browser – GrameneMart – FTP site – Public MySQL

2013 GrameneMart Use case: Find transcription factors having “stop_gained” alleles Custom queries for data mining Gene-based & SNP-based queries Map, markers, and QTL data

2013 FTP site & MySQL server FTP site for bulk downloads: ftp://ftp.gramene.org/pub/gramene/ > mysql -hgramenedb.gramene.org -pgramene

2013 Gramene offers… Genome sequence & gene annotations Comparative analysis Tools & services Metabolic & regulatory pathways – BioCyc platform – Plant Reactome

2013 BioCyc-formatted Pathway DBs Developed by Gramene

2013 Pathway Database Browse Options Download to get a stand alone copy of the RiceCyc database

2013 Gibberellin Biosynthesis I (non C-3, non C-13 hydroxylation) Manual Curation? Evidence / Support Manual Curation? Evidence / Support Enzyme Zoom up to chemical structures Compound / Metabolite

2013 Object Comparison Organism Selection page Comparison of a Metabolic Pathway Across Species Click to visit pathway Click to visit the Gene/ gene product Click to visit the reaction

2013 Pathways BioCyc databases Plant Reactome – 129 rice pathways – Arabidopsis, maize, other plant models

2013

Search for pathways, reactions, and genes

2013 Advanced Search

2013 Synergy between Gramene & iPlant Genetic variation data submission – VCF formatting of data for import into Ensembl Variation repository Representation of the Pan-Genome – Large computational cost of genetic (k-mer) mapping BioCyc-formatted databases to be served from an iPlant virtual server

2013 SAB 2013 Acknowledgements Doreen Ware, PI (USDA ARS, CSHL) Yinping Jiao, Sunita Kumari, Zhenyuan Lu, Marcela K. Monaco, Andrew Olson, Shiran Pasternak, Joshua Stein, Jim Thomason, Sharon Wei, Ken Youens-Clark, Bo Wang, Liya Wang Pankaj Jaiswal, Co-PI (OSU) Vindhya Amarasinghe, Palitha Dharmawardhana, Sushma Naithani, Justin Preece Paul Kersey / Helen Parkinson (EMBL-EBI) Dan Bolser, Arnaud Kerhornou, Dan Staines, Brandon Walts / Nuno Fonseca, Maria Keays, Robert Petrysyk, Eleanor Williams Lincoln Stein (OICR) Robin Haw; Peter D’Eustachio (NYU); Guanming Wu; David Croft (EBI) Crispin Taylor (ASPB) Patty Lockhart